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EXERCISE 3 - pathways.ipynb
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"<img style=\"float: right;\" src=\"files/thehyve_logo.png\">\n",
"# Pathway analysis\n",
"---------------\n",
"Copyright (c) 2015 The Hyve B.V. This notebook is licensed under the GNU General Public License, version 3. Authors: Ruslan Forostianov, Pieter Lukasse."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Before running other code cells: Authenticate with tranSMART"
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Username:admin\n",
"Password:········\n"
]
},
{
"data": {
"text/plain": [
"'SUCCESS'"
]
},
"execution_count": 25,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"import getpass\n",
"from transmart_api import TransmartApi\n",
"\n",
"api = TransmartApi(\n",
" host = 'http://localhost:8080',\n",
" user = raw_input('Username:'),\n",
" password = getpass.getpass('Password:'))\n",
"\n",
"api.access()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Part 1\n",
"------------------------------\n",
"## Get observations data\n",
"\n",
"We start by importing pandas utility package:"
]
},
{
"cell_type": "code",
"execution_count": 26,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"import pandas\n",
"\n",
"pandas.set_option('max_colwidth', 1000)\n",
"pandas.set_option(\"display.max_rows\",100)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Pandas is useful for converting the JSON format, received by the REST API, into an easy to use Python [Pandas DataFrame object](http://pandas.pydata.org/pandas-docs/stable/generated/pandas.DataFrame.html)."
]
},
{
"cell_type": "code",
"execution_count": 28,
"metadata": {
"collapsed": false,
"scrolled": false
},
"outputs": [],
"source": [
"from pandas.io.json import json_normalize\n",
"\n",
"study_id = 'GSE8581'\n",
"obs = api.get_observations(study = study_id)\n",
"obs_df1 = json_normalize(obs)"
]
},
{
"cell_type": "code",
"execution_count": 29,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>label</th>\n",
" <th>subject.age</th>\n",
" <th>subject.birthDate</th>\n",
" <th>subject.deathDate</th>\n",
" <th>subject.id</th>\n",
" <th>subject.inTrialId</th>\n",
" <th>subject.maritalStatus</th>\n",
" <th>subject.race</th>\n",
" <th>subject.religion</th>\n",
" <th>subject.sex</th>\n",
" <th>subject.trial</th>\n",
" <th>value</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>\\Public Studies\\GSE8581\\Biomarker Data\\GPL570\\</td>\n",
" <td>65</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384597</td>\n",
" <td>GSE8581GSM210006</td>\n",
" <td>None</td>\n",
" <td>Afro American</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\Diagnosis\\</td>\n",
" <td>65</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384597</td>\n",
" <td>GSE8581GSM210006</td>\n",
" <td>None</td>\n",
" <td>Afro American</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\FEV1\\</td>\n",
" <td>65</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384597</td>\n",
" <td>GSE8581GSM210006</td>\n",
" <td>None</td>\n",
" <td>Afro American</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>1.41</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\Forced Expiratory Volume Ratio\\</td>\n",
" <td>65</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384597</td>\n",
" <td>GSE8581GSM210006</td>\n",
" <td>None</td>\n",
" <td>Afro American</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>51</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Age\\</td>\n",
" <td>65</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384597</td>\n",
" <td>GSE8581GSM210006</td>\n",
" <td>None</td>\n",
" <td>Afro American</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>65</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Height (inch)\\</td>\n",
" <td>65</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384597</td>\n",
" <td>GSE8581GSM210006</td>\n",
" <td>None</td>\n",
" <td>Afro American</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>66</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Lung Disease\\</td>\n",
" <td>65</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384597</td>\n",
" <td>GSE8581GSM210006</td>\n",
" <td>None</td>\n",
" <td>Afro American</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>chronic obstructive pulmonary disease</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Organism\\</td>\n",
" <td>65</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384597</td>\n",
" <td>GSE8581GSM210006</td>\n",
" <td>None</td>\n",
" <td>Afro American</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>Homo sapiens</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Race\\</td>\n",
" <td>65</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384597</td>\n",
" <td>GSE8581GSM210006</td>\n",
" <td>None</td>\n",
" <td>Afro American</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>Afro American</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Sex\\</td>\n",
" <td>65</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384597</td>\n",
" <td>GSE8581GSM210006</td>\n",
" <td>None</td>\n",
" <td>Afro American</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>\\Public Studies\\GSE8581\\Biomarker Data\\GPL570\\</td>\n",
" <td>77</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384598</td>\n",
" <td>GSE8581GSM212788</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>E</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\Diagnosis\\</td>\n",
" <td>77</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384598</td>\n",
" <td>GSE8581GSM212788</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\FEV1\\</td>\n",
" <td>77</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384598</td>\n",
" <td>GSE8581GSM212788</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>1.29</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\Forced Expiratory Volume Ratio\\</td>\n",
" <td>77</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384598</td>\n",
" <td>GSE8581GSM212788</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>53</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Age\\</td>\n",
" <td>77</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384598</td>\n",
" <td>GSE8581GSM212788</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>77</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Height (inch)\\</td>\n",
" <td>77</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384598</td>\n",
" <td>GSE8581GSM212788</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>67</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Lung Disease\\</td>\n",
" <td>77</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384598</td>\n",
" <td>GSE8581GSM212788</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>chronic obstructive pulmonary disease</td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Organism\\</td>\n",
" <td>77</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384598</td>\n",
" <td>GSE8581GSM212788</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>Homo sapiens</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Race\\</td>\n",
" <td>77</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384598</td>\n",
" <td>GSE8581GSM212788</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>Caucasian</td>\n",
" </tr>\n",
" <tr>\n",
" <th>19</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Sex\\</td>\n",
" <td>77</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384598</td>\n",
" <td>GSE8581GSM212788</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>20</th>\n",
" <td>\\Public Studies\\GSE8581\\Biomarker Data\\GPL570\\</td>\n",
" <td>55</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384599</td>\n",
" <td>GSE8581GSM212067</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>E</td>\n",
" </tr>\n",
" <tr>\n",
" <th>21</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\Diagnosis\\</td>\n",
" <td>55</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384599</td>\n",
" <td>GSE8581GSM212067</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>inflammation</td>\n",
" </tr>\n",
" <tr>\n",
" <th>22</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\FEV1\\</td>\n",
" <td>55</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384599</td>\n",
" <td>GSE8581GSM212067</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>4.04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\Forced Expiratory Volume Ratio\\</td>\n",
" <td>55</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384599</td>\n",
" <td>GSE8581GSM212067</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>79</td>\n",
" </tr>\n",
" <tr>\n",
" <th>24</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Age\\</td>\n",
" <td>55</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384599</td>\n",
" <td>GSE8581GSM212067</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>55</td>\n",
" </tr>\n",
" <tr>\n",
" <th>25</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Height (inch)\\</td>\n",
" <td>55</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384599</td>\n",
" <td>GSE8581GSM212067</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>69</td>\n",
" </tr>\n",
" <tr>\n",
" <th>26</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Lung Disease\\</td>\n",
" <td>55</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384599</td>\n",
" <td>GSE8581GSM212067</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>control</td>\n",
" </tr>\n",
" <tr>\n",
" <th>27</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Organism\\</td>\n",
" <td>55</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384599</td>\n",
" <td>GSE8581GSM212067</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>Homo sapiens</td>\n",
" </tr>\n",
" <tr>\n",
" <th>28</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Race\\</td>\n",
" <td>55</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384599</td>\n",
" <td>GSE8581GSM212067</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>Caucasian</td>\n",
" </tr>\n",
" <tr>\n",
" <th>29</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Sex\\</td>\n",
" <td>55</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384599</td>\n",
" <td>GSE8581GSM212067</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>30</th>\n",
" <td>\\Public Studies\\GSE8581\\Biomarker Data\\GPL570\\</td>\n",
" <td>64</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384600</td>\n",
" <td>GSE8581GSM212074</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>E</td>\n",
" </tr>\n",
" <tr>\n",
" <th>31</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\Diagnosis\\</td>\n",
" <td>64</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384600</td>\n",
" <td>GSE8581GSM212074</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>32</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\FEV1\\</td>\n",
" <td>64</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384600</td>\n",
" <td>GSE8581GSM212074</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>2.06</td>\n",
" </tr>\n",
" <tr>\n",
" <th>33</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\Forced Expiratory Volume Ratio\\</td>\n",
" <td>64</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384600</td>\n",
" <td>GSE8581GSM212074</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>54</td>\n",
" </tr>\n",
" <tr>\n",
" <th>34</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Age\\</td>\n",
" <td>64</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384600</td>\n",
" <td>GSE8581GSM212074</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>64</td>\n",
" </tr>\n",
" <tr>\n",
" <th>35</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Height (inch)\\</td>\n",
" <td>64</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384600</td>\n",
" <td>GSE8581GSM212074</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>65</td>\n",
" </tr>\n",
" <tr>\n",
" <th>36</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Lung Disease\\</td>\n",
" <td>64</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384600</td>\n",
" <td>GSE8581GSM212074</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>chronic obstructive pulmonary disease</td>\n",
" </tr>\n",
" <tr>\n",
" <th>37</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Organism\\</td>\n",
" <td>64</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384600</td>\n",
" <td>GSE8581GSM212074</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>Homo sapiens</td>\n",
" </tr>\n",
" <tr>\n",
" <th>38</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Race\\</td>\n",
" <td>64</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384600</td>\n",
" <td>GSE8581GSM212074</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>Caucasian</td>\n",
" </tr>\n",
" <tr>\n",
" <th>39</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Sex\\</td>\n",
" <td>64</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384600</td>\n",
" <td>GSE8581GSM212074</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>40</th>\n",
" <td>\\Public Studies\\GSE8581\\Biomarker Data\\GPL570\\</td>\n",
" <td>77</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384601</td>\n",
" <td>GSE8581GSM213037</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>E</td>\n",
" </tr>\n",
" <tr>\n",
" <th>41</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\Diagnosis\\</td>\n",
" <td>77</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384601</td>\n",
" <td>GSE8581GSM213037</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\FEV1\\</td>\n",
" <td>77</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384601</td>\n",
" <td>GSE8581GSM213037</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>2.25</td>\n",
" </tr>\n",
" <tr>\n",
" <th>43</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\Forced Expiratory Volume Ratio\\</td>\n",
" <td>77</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384601</td>\n",
" <td>GSE8581GSM213037</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>72</td>\n",
" </tr>\n",
" <tr>\n",
" <th>44</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Age\\</td>\n",
" <td>77</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384601</td>\n",
" <td>GSE8581GSM213037</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>77</td>\n",
" </tr>\n",
" <tr>\n",
" <th>45</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Height (inch)\\</td>\n",
" <td>77</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384601</td>\n",
" <td>GSE8581GSM213037</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>66</td>\n",
" </tr>\n",
" <tr>\n",
" <th>46</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Lung Disease\\</td>\n",
" <td>77</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384601</td>\n",
" <td>GSE8581GSM213037</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>not specified</td>\n",
" </tr>\n",
" <tr>\n",
" <th>47</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Organism\\</td>\n",
" <td>77</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384601</td>\n",
" <td>GSE8581GSM213037</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>Homo sapiens</td>\n",
" </tr>\n",
" <tr>\n",
" <th>48</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Race\\</td>\n",
" <td>77</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384601</td>\n",
" <td>GSE8581GSM213037</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>Caucasian</td>\n",
" </tr>\n",
" <tr>\n",
" <th>49</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Sex\\</td>\n",
" <td>77</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384601</td>\n",
" <td>GSE8581GSM213037</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>530</th>\n",
" <td>\\Public Studies\\GSE8581\\Biomarker Data\\GPL570\\</td>\n",
" <td>63</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384650</td>\n",
" <td>GSE8581GSM210004</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>531</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\Diagnosis\\</td>\n",
" <td>63</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384650</td>\n",
" <td>GSE8581GSM210004</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>532</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\FEV1\\</td>\n",
" <td>63</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384650</td>\n",
" <td>GSE8581GSM210004</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>2.54</td>\n",
" </tr>\n",
" <tr>\n",
" <th>533</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\Forced Expiratory Volume Ratio\\</td>\n",
" <td>63</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384650</td>\n",
" <td>GSE8581GSM210004</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>58</td>\n",
" </tr>\n",
" <tr>\n",
" <th>534</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Age\\</td>\n",
" <td>63</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384650</td>\n",
" <td>GSE8581GSM210004</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>63</td>\n",
" </tr>\n",
" <tr>\n",
" <th>535</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Height (inch)\\</td>\n",
" <td>63</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384650</td>\n",
" <td>GSE8581GSM210004</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>72</td>\n",
" </tr>\n",
" <tr>\n",
" <th>536</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Lung Disease\\</td>\n",
" <td>63</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384650</td>\n",
" <td>GSE8581GSM210004</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>chronic obstructive pulmonary disease</td>\n",
" </tr>\n",
" <tr>\n",
" <th>537</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Organism\\</td>\n",
" <td>63</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384650</td>\n",
" <td>GSE8581GSM210004</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>Homo sapiens</td>\n",
" </tr>\n",
" <tr>\n",
" <th>538</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Race\\</td>\n",
" <td>63</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384650</td>\n",
" <td>GSE8581GSM210004</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>Caucasian</td>\n",
" </tr>\n",
" <tr>\n",
" <th>539</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Sex\\</td>\n",
" <td>63</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384650</td>\n",
" <td>GSE8581GSM210004</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>MALE</td>\n",
" <td>GSE8581</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>540</th>\n",
" <td>\\Public Studies\\GSE8581\\Biomarker Data\\GPL570\\</td>\n",
" <td>67</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384651</td>\n",
" <td>GSE8581GSM210193</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>E</td>\n",
" </tr>\n",
" <tr>\n",
" <th>541</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\Diagnosis\\</td>\n",
" <td>67</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384651</td>\n",
" <td>GSE8581GSM210193</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>Unknown</td>\n",
" </tr>\n",
" <tr>\n",
" <th>542</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\FEV1\\</td>\n",
" <td>67</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384651</td>\n",
" <td>GSE8581GSM210193</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>1.63</td>\n",
" </tr>\n",
" <tr>\n",
" <th>543</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\Forced Expiratory Volume Ratio\\</td>\n",
" <td>67</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384651</td>\n",
" <td>GSE8581GSM210193</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>80.78</td>\n",
" </tr>\n",
" <tr>\n",
" <th>544</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Age\\</td>\n",
" <td>67</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384651</td>\n",
" <td>GSE8581GSM210193</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>67</td>\n",
" </tr>\n",
" <tr>\n",
" <th>545</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Height (inch)\\</td>\n",
" <td>67</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384651</td>\n",
" <td>GSE8581GSM210193</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>66</td>\n",
" </tr>\n",
" <tr>\n",
" <th>546</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Lung Disease\\</td>\n",
" <td>67</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384651</td>\n",
" <td>GSE8581GSM210193</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>not specified</td>\n",
" </tr>\n",
" <tr>\n",
" <th>547</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Organism\\</td>\n",
" <td>67</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384651</td>\n",
" <td>GSE8581GSM210193</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>Homo sapiens</td>\n",
" </tr>\n",
" <tr>\n",
" <th>548</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Race\\</td>\n",
" <td>67</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384651</td>\n",
" <td>GSE8581GSM210193</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>Caucasian</td>\n",
" </tr>\n",
" <tr>\n",
" <th>549</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Sex\\</td>\n",
" <td>67</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384651</td>\n",
" <td>GSE8581GSM210193</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>550</th>\n",
" <td>\\Public Studies\\GSE8581\\Biomarker Data\\GPL570\\</td>\n",
" <td>61</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384652</td>\n",
" <td>GSE8581GSM212809</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>E</td>\n",
" </tr>\n",
" <tr>\n",
" <th>551</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\Diagnosis\\</td>\n",
" <td>61</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384652</td>\n",
" <td>GSE8581GSM212809</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>552</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\FEV1\\</td>\n",
" <td>61</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384652</td>\n",
" <td>GSE8581GSM212809</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>1.28</td>\n",
" </tr>\n",
" <tr>\n",
" <th>553</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\Forced Expiratory Volume Ratio\\</td>\n",
" <td>61</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384652</td>\n",
" <td>GSE8581GSM212809</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>89</td>\n",
" </tr>\n",
" <tr>\n",
" <th>554</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Age\\</td>\n",
" <td>61</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384652</td>\n",
" <td>GSE8581GSM212809</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>61</td>\n",
" </tr>\n",
" <tr>\n",
" <th>555</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Height (inch)\\</td>\n",
" <td>61</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384652</td>\n",
" <td>GSE8581GSM212809</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>65</td>\n",
" </tr>\n",
" <tr>\n",
" <th>556</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Lung Disease\\</td>\n",
" <td>61</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384652</td>\n",
" <td>GSE8581GSM212809</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>not specified</td>\n",
" </tr>\n",
" <tr>\n",
" <th>557</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Organism\\</td>\n",
" <td>61</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384652</td>\n",
" <td>GSE8581GSM212809</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>Homo sapiens</td>\n",
" </tr>\n",
" <tr>\n",
" <th>558</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Race\\</td>\n",
" <td>61</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384652</td>\n",
" <td>GSE8581GSM212809</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>Caucasian</td>\n",
" </tr>\n",
" <tr>\n",
" <th>559</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Sex\\</td>\n",
" <td>61</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384652</td>\n",
" <td>GSE8581GSM212809</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>560</th>\n",
" <td>\\Public Studies\\GSE8581\\Biomarker Data\\GPL570\\</td>\n",
" <td>57</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384653</td>\n",
" <td>GSE8581GSM210196</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>E</td>\n",
" </tr>\n",
" <tr>\n",
" <th>561</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\Diagnosis\\</td>\n",
" <td>57</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384653</td>\n",
" <td>GSE8581GSM210196</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>562</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\FEV1\\</td>\n",
" <td>57</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384653</td>\n",
" <td>GSE8581GSM210196</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>2.3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>563</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\Forced Expiratory Volume Ratio\\</td>\n",
" <td>57</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384653</td>\n",
" <td>GSE8581GSM210196</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>74</td>\n",
" </tr>\n",
" <tr>\n",
" <th>564</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Age\\</td>\n",
" <td>57</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384653</td>\n",
" <td>GSE8581GSM210196</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>57</td>\n",
" </tr>\n",
" <tr>\n",
" <th>565</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Height (inch)\\</td>\n",
" <td>57</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384653</td>\n",
" <td>GSE8581GSM210196</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>65</td>\n",
" </tr>\n",
" <tr>\n",
" <th>566</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Lung Disease\\</td>\n",
" <td>57</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384653</td>\n",
" <td>GSE8581GSM210196</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>control</td>\n",
" </tr>\n",
" <tr>\n",
" <th>567</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Organism\\</td>\n",
" <td>57</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384653</td>\n",
" <td>GSE8581GSM210196</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>Homo sapiens</td>\n",
" </tr>\n",
" <tr>\n",
" <th>568</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Race\\</td>\n",
" <td>57</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384653</td>\n",
" <td>GSE8581GSM210196</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>Caucasian</td>\n",
" </tr>\n",
" <tr>\n",
" <th>569</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Sex\\</td>\n",
" <td>57</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384653</td>\n",
" <td>GSE8581GSM210196</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>570</th>\n",
" <td>\\Public Studies\\GSE8581\\Biomarker Data\\GPL570\\</td>\n",
" <td>54</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384654</td>\n",
" <td>GSE8581GSM212790</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>E</td>\n",
" </tr>\n",
" <tr>\n",
" <th>571</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\Diagnosis\\</td>\n",
" <td>54</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384654</td>\n",
" <td>GSE8581GSM212790</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>572</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\FEV1\\</td>\n",
" <td>54</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384654</td>\n",
" <td>GSE8581GSM212790</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>2.83</td>\n",
" </tr>\n",
" <tr>\n",
" <th>573</th>\n",
" <td>\\Public Studies\\GSE8581\\Endpoints\\Forced Expiratory Volume Ratio\\</td>\n",
" <td>54</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384654</td>\n",
" <td>GSE8581GSM212790</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>75</td>\n",
" </tr>\n",
" <tr>\n",
" <th>574</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Age\\</td>\n",
" <td>54</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384654</td>\n",
" <td>GSE8581GSM212790</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>54</td>\n",
" </tr>\n",
" <tr>\n",
" <th>575</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Height (inch)\\</td>\n",
" <td>54</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384654</td>\n",
" <td>GSE8581GSM212790</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>75</td>\n",
" </tr>\n",
" <tr>\n",
" <th>576</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Lung Disease\\</td>\n",
" <td>54</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384654</td>\n",
" <td>GSE8581GSM212790</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>control</td>\n",
" </tr>\n",
" <tr>\n",
" <th>577</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Organism\\</td>\n",
" <td>54</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384654</td>\n",
" <td>GSE8581GSM212790</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>Homo sapiens</td>\n",
" </tr>\n",
" <tr>\n",
" <th>578</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Race\\</td>\n",
" <td>54</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384654</td>\n",
" <td>GSE8581GSM212790</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>Caucasian</td>\n",
" </tr>\n",
" <tr>\n",
" <th>579</th>\n",
" <td>\\Public Studies\\GSE8581\\Subjects\\Sex\\</td>\n",
" <td>54</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>1000384654</td>\n",
" <td>GSE8581GSM212790</td>\n",
" <td>None</td>\n",
" <td>Caucasian</td>\n",
" <td>None</td>\n",
" <td>FEMALE</td>\n",
" <td>GSE8581</td>\n",
" <td>female</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>580 rows × 12 columns</p>\n",
"</div>"
],
"text/plain": [
" label \\\n",
"0 \\Public Studies\\GSE8581\\Biomarker Data\\GPL570\\ \n",
"1 \\Public Studies\\GSE8581\\Endpoints\\Diagnosis\\ \n",
"2 \\Public Studies\\GSE8581\\Endpoints\\FEV1\\ \n",
"3 \\Public Studies\\GSE8581\\Endpoints\\Forced Expiratory Volume Ratio\\ \n",
"4 \\Public Studies\\GSE8581\\Subjects\\Age\\ \n",
"5 \\Public Studies\\GSE8581\\Subjects\\Height (inch)\\ \n",
"6 \\Public Studies\\GSE8581\\Subjects\\Lung Disease\\ \n",
"7 \\Public Studies\\GSE8581\\Subjects\\Organism\\ \n",
"8 \\Public Studies\\GSE8581\\Subjects\\Race\\ \n",
"9 \\Public Studies\\GSE8581\\Subjects\\Sex\\ \n",
"10 \\Public Studies\\GSE8581\\Biomarker Data\\GPL570\\ \n",
"11 \\Public Studies\\GSE8581\\Endpoints\\Diagnosis\\ \n",
"12 \\Public Studies\\GSE8581\\Endpoints\\FEV1\\ \n",
"13 \\Public Studies\\GSE8581\\Endpoints\\Forced Expiratory Volume Ratio\\ \n",
"14 \\Public Studies\\GSE8581\\Subjects\\Age\\ \n",
"15 \\Public Studies\\GSE8581\\Subjects\\Height (inch)\\ \n",
"16 \\Public Studies\\GSE8581\\Subjects\\Lung Disease\\ \n",
"17 \\Public Studies\\GSE8581\\Subjects\\Organism\\ \n",
"18 \\Public Studies\\GSE8581\\Subjects\\Race\\ \n",
"19 \\Public Studies\\GSE8581\\Subjects\\Sex\\ \n",
"20 \\Public Studies\\GSE8581\\Biomarker Data\\GPL570\\ \n",
"21 \\Public Studies\\GSE8581\\Endpoints\\Diagnosis\\ \n",
"22 \\Public Studies\\GSE8581\\Endpoints\\FEV1\\ \n",
"23 \\Public Studies\\GSE8581\\Endpoints\\Forced Expiratory Volume Ratio\\ \n",
"24 \\Public Studies\\GSE8581\\Subjects\\Age\\ \n",
"25 \\Public Studies\\GSE8581\\Subjects\\Height (inch)\\ \n",
"26 \\Public Studies\\GSE8581\\Subjects\\Lung Disease\\ \n",
"27 \\Public Studies\\GSE8581\\Subjects\\Organism\\ \n",
"28 \\Public Studies\\GSE8581\\Subjects\\Race\\ \n",
"29 \\Public Studies\\GSE8581\\Subjects\\Sex\\ \n",
"30 \\Public Studies\\GSE8581\\Biomarker Data\\GPL570\\ \n",
"31 \\Public Studies\\GSE8581\\Endpoints\\Diagnosis\\ \n",
"32 \\Public Studies\\GSE8581\\Endpoints\\FEV1\\ \n",
"33 \\Public Studies\\GSE8581\\Endpoints\\Forced Expiratory Volume Ratio\\ \n",
"34 \\Public Studies\\GSE8581\\Subjects\\Age\\ \n",
"35 \\Public Studies\\GSE8581\\Subjects\\Height (inch)\\ \n",
"36 \\Public Studies\\GSE8581\\Subjects\\Lung Disease\\ \n",
"37 \\Public Studies\\GSE8581\\Subjects\\Organism\\ \n",
"38 \\Public Studies\\GSE8581\\Subjects\\Race\\ \n",
"39 \\Public Studies\\GSE8581\\Subjects\\Sex\\ \n",
"40 \\Public Studies\\GSE8581\\Biomarker Data\\GPL570\\ \n",
"41 \\Public Studies\\GSE8581\\Endpoints\\Diagnosis\\ \n",
"42 \\Public Studies\\GSE8581\\Endpoints\\FEV1\\ \n",
"43 \\Public Studies\\GSE8581\\Endpoints\\Forced Expiratory Volume Ratio\\ \n",
"44 \\Public Studies\\GSE8581\\Subjects\\Age\\ \n",
"45 \\Public Studies\\GSE8581\\Subjects\\Height (inch)\\ \n",
"46 \\Public Studies\\GSE8581\\Subjects\\Lung Disease\\ \n",
"47 \\Public Studies\\GSE8581\\Subjects\\Organism\\ \n",
"48 \\Public Studies\\GSE8581\\Subjects\\Race\\ \n",
"49 \\Public Studies\\GSE8581\\Subjects\\Sex\\ \n",
".. ... \n",
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"533 \\Public Studies\\GSE8581\\Endpoints\\Forced Expiratory Volume Ratio\\ \n",
"534 \\Public Studies\\GSE8581\\Subjects\\Age\\ \n",
"535 \\Public Studies\\GSE8581\\Subjects\\Height (inch)\\ \n",
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"538 \\Public Studies\\GSE8581\\Subjects\\Race\\ \n",
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"544 \\Public Studies\\GSE8581\\Subjects\\Age\\ \n",
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"546 \\Public Studies\\GSE8581\\Subjects\\Lung Disease\\ \n",
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"\n",
" subject.age subject.birthDate subject.deathDate subject.id \\\n",
"0 65 None None 1000384597 \n",
"1 65 None None 1000384597 \n",
"2 65 None None 1000384597 \n",
"3 65 None None 1000384597 \n",
"4 65 None None 1000384597 \n",
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"8 65 None None 1000384597 \n",
"9 65 None None 1000384597 \n",
"10 77 None None 1000384598 \n",
"11 77 None None 1000384598 \n",
"12 77 None None 1000384598 \n",
"13 77 None None 1000384598 \n",
"14 77 None None 1000384598 \n",
"15 77 None None 1000384598 \n",
"16 77 None None 1000384598 \n",
"17 77 None None 1000384598 \n",
"18 77 None None 1000384598 \n",
"19 77 None None 1000384598 \n",
"20 55 None None 1000384599 \n",
"21 55 None None 1000384599 \n",
"22 55 None None 1000384599 \n",
"23 55 None None 1000384599 \n",
"24 55 None None 1000384599 \n",
"25 55 None None 1000384599 \n",
"26 55 None None 1000384599 \n",
"27 55 None None 1000384599 \n",
"28 55 None None 1000384599 \n",
"29 55 None None 1000384599 \n",
"30 64 None None 1000384600 \n",
"31 64 None None 1000384600 \n",
"32 64 None None 1000384600 \n",
"33 64 None None 1000384600 \n",
"34 64 None None 1000384600 \n",
"35 64 None None 1000384600 \n",
"36 64 None None 1000384600 \n",
"37 64 None None 1000384600 \n",
"38 64 None None 1000384600 \n",
"39 64 None None 1000384600 \n",
"40 77 None None 1000384601 \n",
"41 77 None None 1000384601 \n",
"42 77 None None 1000384601 \n",
"43 77 None None 1000384601 \n",
"44 77 None None 1000384601 \n",
"45 77 None None 1000384601 \n",
"46 77 None None 1000384601 \n",
"47 77 None None 1000384601 \n",
"48 77 None None 1000384601 \n",
"49 77 None None 1000384601 \n",
".. ... ... ... ... \n",
"530 63 None None 1000384650 \n",
"531 63 None None 1000384650 \n",
"532 63 None None 1000384650 \n",
"533 63 None None 1000384650 \n",
"534 63 None None 1000384650 \n",
"535 63 None None 1000384650 \n",
"536 63 None None 1000384650 \n",
"537 63 None None 1000384650 \n",
"538 63 None None 1000384650 \n",
"539 63 None None 1000384650 \n",
"540 67 None None 1000384651 \n",
"541 67 None None 1000384651 \n",
"542 67 None None 1000384651 \n",
"543 67 None None 1000384651 \n",
"544 67 None None 1000384651 \n",
"545 67 None None 1000384651 \n",
"546 67 None None 1000384651 \n",
"547 67 None None 1000384651 \n",
"548 67 None None 1000384651 \n",
"549 67 None None 1000384651 \n",
"550 61 None None 1000384652 \n",
"551 61 None None 1000384652 \n",
"552 61 None None 1000384652 \n",
"553 61 None None 1000384652 \n",
"554 61 None None 1000384652 \n",
"555 61 None None 1000384652 \n",
"556 61 None None 1000384652 \n",
"557 61 None None 1000384652 \n",
"558 61 None None 1000384652 \n",
"559 61 None None 1000384652 \n",
"560 57 None None 1000384653 \n",
"561 57 None None 1000384653 \n",
"562 57 None None 1000384653 \n",
"563 57 None None 1000384653 \n",
"564 57 None None 1000384653 \n",
"565 57 None None 1000384653 \n",
"566 57 None None 1000384653 \n",
"567 57 None None 1000384653 \n",
"568 57 None None 1000384653 \n",
"569 57 None None 1000384653 \n",
"570 54 None None 1000384654 \n",
"571 54 None None 1000384654 \n",
"572 54 None None 1000384654 \n",
"573 54 None None 1000384654 \n",
"574 54 None None 1000384654 \n",
"575 54 None None 1000384654 \n",
"576 54 None None 1000384654 \n",
"577 54 None None 1000384654 \n",
"578 54 None None 1000384654 \n",
"579 54 None None 1000384654 \n",
"\n",
" subject.inTrialId subject.maritalStatus subject.race subject.religion \\\n",
"0 GSE8581GSM210006 None Afro American None \n",
"1 GSE8581GSM210006 None Afro American None \n",
"2 GSE8581GSM210006 None Afro American None \n",
"3 GSE8581GSM210006 None Afro American None \n",
"4 GSE8581GSM210006 None Afro American None \n",
"5 GSE8581GSM210006 None Afro American None \n",
"6 GSE8581GSM210006 None Afro American None \n",
"7 GSE8581GSM210006 None Afro American None \n",
"8 GSE8581GSM210006 None Afro American None \n",
"9 GSE8581GSM210006 None Afro American None \n",
"10 GSE8581GSM212788 None Caucasian None \n",
"11 GSE8581GSM212788 None Caucasian None \n",
"12 GSE8581GSM212788 None Caucasian None \n",
"13 GSE8581GSM212788 None Caucasian None \n",
"14 GSE8581GSM212788 None Caucasian None \n",
"15 GSE8581GSM212788 None Caucasian None \n",
"16 GSE8581GSM212788 None Caucasian None \n",
"17 GSE8581GSM212788 None Caucasian None \n",
"18 GSE8581GSM212788 None Caucasian None \n",
"19 GSE8581GSM212788 None Caucasian None \n",
"20 GSE8581GSM212067 None Caucasian None \n",
"21 GSE8581GSM212067 None Caucasian None \n",
"22 GSE8581GSM212067 None Caucasian None \n",
"23 GSE8581GSM212067 None Caucasian None \n",
"24 GSE8581GSM212067 None Caucasian None \n",
"25 GSE8581GSM212067 None Caucasian None \n",
"26 GSE8581GSM212067 None Caucasian None \n",
"27 GSE8581GSM212067 None Caucasian None \n",
"28 GSE8581GSM212067 None Caucasian None \n",
"29 GSE8581GSM212067 None Caucasian None \n",
"30 GSE8581GSM212074 None Caucasian None \n",
"31 GSE8581GSM212074 None Caucasian None \n",
"32 GSE8581GSM212074 None Caucasian None \n",
"33 GSE8581GSM212074 None Caucasian None \n",
"34 GSE8581GSM212074 None Caucasian None \n",
"35 GSE8581GSM212074 None Caucasian None \n",
"36 GSE8581GSM212074 None Caucasian None \n",
"37 GSE8581GSM212074 None Caucasian None \n",
"38 GSE8581GSM212074 None Caucasian None \n",
"39 GSE8581GSM212074 None Caucasian None \n",
"40 GSE8581GSM213037 None Caucasian None \n",
"41 GSE8581GSM213037 None Caucasian None \n",
"42 GSE8581GSM213037 None Caucasian None \n",
"43 GSE8581GSM213037 None Caucasian None \n",
"44 GSE8581GSM213037 None Caucasian None \n",
"45 GSE8581GSM213037 None Caucasian None \n",
"46 GSE8581GSM213037 None Caucasian None \n",
"47 GSE8581GSM213037 None Caucasian None \n",
"48 GSE8581GSM213037 None Caucasian None \n",
"49 GSE8581GSM213037 None Caucasian None \n",
".. ... ... ... ... \n",
"530 GSE8581GSM210004 None Caucasian None \n",
"531 GSE8581GSM210004 None Caucasian None \n",
"532 GSE8581GSM210004 None Caucasian None \n",
"533 GSE8581GSM210004 None Caucasian None \n",
"534 GSE8581GSM210004 None Caucasian None \n",
"535 GSE8581GSM210004 None Caucasian None \n",
"536 GSE8581GSM210004 None Caucasian None \n",
"537 GSE8581GSM210004 None Caucasian None \n",
"538 GSE8581GSM210004 None Caucasian None \n",
"539 GSE8581GSM210004 None Caucasian None \n",
"540 GSE8581GSM210193 None Caucasian None \n",
"541 GSE8581GSM210193 None Caucasian None \n",
"542 GSE8581GSM210193 None Caucasian None \n",
"543 GSE8581GSM210193 None Caucasian None \n",
"544 GSE8581GSM210193 None Caucasian None \n",
"545 GSE8581GSM210193 None Caucasian None \n",
"546 GSE8581GSM210193 None Caucasian None \n",
"547 GSE8581GSM210193 None Caucasian None \n",
"548 GSE8581GSM210193 None Caucasian None \n",
"549 GSE8581GSM210193 None Caucasian None \n",
"550 GSE8581GSM212809 None Caucasian None \n",
"551 GSE8581GSM212809 None Caucasian None \n",
"552 GSE8581GSM212809 None Caucasian None \n",
"553 GSE8581GSM212809 None Caucasian None \n",
"554 GSE8581GSM212809 None Caucasian None \n",
"555 GSE8581GSM212809 None Caucasian None \n",
"556 GSE8581GSM212809 None Caucasian None \n",
"557 GSE8581GSM212809 None Caucasian None \n",
"558 GSE8581GSM212809 None Caucasian None \n",
"559 GSE8581GSM212809 None Caucasian None \n",
"560 GSE8581GSM210196 None Caucasian None \n",
"561 GSE8581GSM210196 None Caucasian None \n",
"562 GSE8581GSM210196 None Caucasian None \n",
"563 GSE8581GSM210196 None Caucasian None \n",
"564 GSE8581GSM210196 None Caucasian None \n",
"565 GSE8581GSM210196 None Caucasian None \n",
"566 GSE8581GSM210196 None Caucasian None \n",
"567 GSE8581GSM210196 None Caucasian None \n",
"568 GSE8581GSM210196 None Caucasian None \n",
"569 GSE8581GSM210196 None Caucasian None \n",
"570 GSE8581GSM212790 None Caucasian None \n",
"571 GSE8581GSM212790 None Caucasian None \n",
"572 GSE8581GSM212790 None Caucasian None \n",
"573 GSE8581GSM212790 None Caucasian None \n",
"574 GSE8581GSM212790 None Caucasian None \n",
"575 GSE8581GSM212790 None Caucasian None \n",
"576 GSE8581GSM212790 None Caucasian None \n",
"577 GSE8581GSM212790 None Caucasian None \n",
"578 GSE8581GSM212790 None Caucasian None \n",
"579 GSE8581GSM212790 None Caucasian None \n",
"\n",
" subject.sex subject.trial value \n",
"0 FEMALE GSE8581 None \n",
"1 FEMALE GSE8581 non-small cell adenocarcinoma \n",
"2 FEMALE GSE8581 1.41 \n",
"3 FEMALE GSE8581 51 \n",
"4 FEMALE GSE8581 65 \n",
"5 FEMALE GSE8581 66 \n",
"6 FEMALE GSE8581 chronic obstructive pulmonary disease \n",
"7 FEMALE GSE8581 Homo sapiens \n",
"8 FEMALE GSE8581 Afro American \n",
"9 FEMALE GSE8581 female \n",
"10 FEMALE GSE8581 E \n",
"11 FEMALE GSE8581 non-small cell squamous cell carcinoma \n",
"12 FEMALE GSE8581 1.29 \n",
"13 FEMALE GSE8581 53 \n",
"14 FEMALE GSE8581 77 \n",
"15 FEMALE GSE8581 67 \n",
"16 FEMALE GSE8581 chronic obstructive pulmonary disease \n",
"17 FEMALE GSE8581 Homo sapiens \n",
"18 FEMALE GSE8581 Caucasian \n",
"19 FEMALE GSE8581 female \n",
"20 MALE GSE8581 E \n",
"21 MALE GSE8581 inflammation \n",
"22 MALE GSE8581 4.04 \n",
"23 MALE GSE8581 79 \n",
"24 MALE GSE8581 55 \n",
"25 MALE GSE8581 69 \n",
"26 MALE GSE8581 control \n",
"27 MALE GSE8581 Homo sapiens \n",
"28 MALE GSE8581 Caucasian \n",
"29 MALE GSE8581 male \n",
"30 MALE GSE8581 E \n",
"31 MALE GSE8581 non-small cell squamous cell carcinoma \n",
"32 MALE GSE8581 2.06 \n",
"33 MALE GSE8581 54 \n",
"34 MALE GSE8581 64 \n",
"35 MALE GSE8581 65 \n",
"36 MALE GSE8581 chronic obstructive pulmonary disease \n",
"37 MALE GSE8581 Homo sapiens \n",
"38 MALE GSE8581 Caucasian \n",
"39 MALE GSE8581 male \n",
"40 MALE GSE8581 E \n",
"41 MALE GSE8581 non-small cell squamous cell carcinoma \n",
"42 MALE GSE8581 2.25 \n",
"43 MALE GSE8581 72 \n",
"44 MALE GSE8581 77 \n",
"45 MALE GSE8581 66 \n",
"46 MALE GSE8581 not specified \n",
"47 MALE GSE8581 Homo sapiens \n",
"48 MALE GSE8581 Caucasian \n",
"49 MALE GSE8581 male \n",
".. ... ... ... \n",
"530 MALE GSE8581 None \n",
"531 MALE GSE8581 non-small cell squamous cell carcinoma \n",
"532 MALE GSE8581 2.54 \n",
"533 MALE GSE8581 58 \n",
"534 MALE GSE8581 63 \n",
"535 MALE GSE8581 72 \n",
"536 MALE GSE8581 chronic obstructive pulmonary disease \n",
"537 MALE GSE8581 Homo sapiens \n",
"538 MALE GSE8581 Caucasian \n",
"539 MALE GSE8581 male \n",
"540 FEMALE GSE8581 E \n",
"541 FEMALE GSE8581 Unknown \n",
"542 FEMALE GSE8581 1.63 \n",
"543 FEMALE GSE8581 80.78 \n",
"544 FEMALE GSE8581 67 \n",
"545 FEMALE GSE8581 66 \n",
"546 FEMALE GSE8581 not specified \n",
"547 FEMALE GSE8581 Homo sapiens \n",
"548 FEMALE GSE8581 Caucasian \n",
"549 FEMALE GSE8581 female \n",
"550 FEMALE GSE8581 E \n",
"551 FEMALE GSE8581 non-small cell adenocarcinoma \n",
"552 FEMALE GSE8581 1.28 \n",
"553 FEMALE GSE8581 89 \n",
"554 FEMALE GSE8581 61 \n",
"555 FEMALE GSE8581 65 \n",
"556 FEMALE GSE8581 not specified \n",
"557 FEMALE GSE8581 Homo sapiens \n",
"558 FEMALE GSE8581 Caucasian \n",
"559 FEMALE GSE8581 female \n",
"560 FEMALE GSE8581 E \n",
"561 FEMALE GSE8581 non-small cell adenocarcinoma \n",
"562 FEMALE GSE8581 2.3 \n",
"563 FEMALE GSE8581 74 \n",
"564 FEMALE GSE8581 57 \n",
"565 FEMALE GSE8581 65 \n",
"566 FEMALE GSE8581 control \n",
"567 FEMALE GSE8581 Homo sapiens \n",
"568 FEMALE GSE8581 Caucasian \n",
"569 FEMALE GSE8581 female \n",
"570 FEMALE GSE8581 E \n",
"571 FEMALE GSE8581 non-small cell squamous cell carcinoma \n",
"572 FEMALE GSE8581 2.83 \n",
"573 FEMALE GSE8581 75 \n",
"574 FEMALE GSE8581 54 \n",
"575 FEMALE GSE8581 75 \n",
"576 FEMALE GSE8581 control \n",
"577 FEMALE GSE8581 Homo sapiens \n",
"578 FEMALE GSE8581 Caucasian \n",
"579 FEMALE GSE8581 female \n",
"\n",
"[580 rows x 12 columns]"
]
},
"execution_count": 29,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"obs_df1"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Here we reorganize the data such that each line represents a subject and the columns represent the different clinical attributes."
]
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th>label</th>\n",
" <th>Biomarker Data\\GPL570</th>\n",
" <th>Endpoints\\Diagnosis</th>\n",
" <th>Endpoints\\FEV1</th>\n",
" <th>Endpoints\\Forced Expiratory Volume Ratio</th>\n",
" <th>Subjects\\Age</th>\n",
" <th>Subjects\\Height (inch)</th>\n",
" <th>Subjects\\Lung Disease</th>\n",
" <th>Subjects\\Organism</th>\n",
" <th>Subjects\\Race</th>\n",
" <th>Subjects\\Sex</th>\n",
" </tr>\n",
" <tr>\n",
" <th>subject.inTrialId</th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>GSE8581GSM210004</th>\n",
" <td>None</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" <td>2.54</td>\n",
" <td>58.00</td>\n",
" <td>63</td>\n",
" <td>72</td>\n",
" <td>chronic obstructive pulmonary disease</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210005</th>\n",
" <td>None</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>1.69</td>\n",
" <td>83.66</td>\n",
" <td>84</td>\n",
" <td>60</td>\n",
" <td>control</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Afro American</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210006</th>\n",
" <td>None</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>1.41</td>\n",
" <td>51.00</td>\n",
" <td>65</td>\n",
" <td>66</td>\n",
" <td>chronic obstructive pulmonary disease</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Afro American</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210007</th>\n",
" <td>E</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>2.51</td>\n",
" <td>80.96</td>\n",
" <td>46</td>\n",
" <td>66</td>\n",
" <td>not specified</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210008</th>\n",
" <td>E</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>1.64</td>\n",
" <td>57.00</td>\n",
" <td>53</td>\n",
" <td>65</td>\n",
" <td>chronic obstructive pulmonary disease</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210009</th>\n",
" <td>E</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" <td>2.72</td>\n",
" <td>74.00</td>\n",
" <td>53</td>\n",
" <td>64</td>\n",
" <td>control</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210010</th>\n",
" <td>E</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>1.45</td>\n",
" <td>73.00</td>\n",
" <td>77</td>\n",
" <td>63</td>\n",
" <td>not specified</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210011</th>\n",
" <td>E</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" <td>1.87</td>\n",
" <td>56.00</td>\n",
" <td>56</td>\n",
" <td>72</td>\n",
" <td>chronic obstructive pulmonary disease</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210012</th>\n",
" <td>E</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>2.76</td>\n",
" <td>70.58</td>\n",
" <td>61</td>\n",
" <td>69</td>\n",
" <td>not specified</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210014</th>\n",
" <td>E</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>1.98</td>\n",
" <td>78.00</td>\n",
" <td>71</td>\n",
" <td>63</td>\n",
" <td>control</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210015</th>\n",
" <td>E</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>2.59</td>\n",
" <td>74.00</td>\n",
" <td>68</td>\n",
" <td>65</td>\n",
" <td>control</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210071</th>\n",
" <td>E</td>\n",
" <td>emphysema</td>\n",
" <td>1.16</td>\n",
" <td>43.00</td>\n",
" <td>68</td>\n",
" <td>67</td>\n",
" <td>chronic obstructive pulmonary disease</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210087</th>\n",
" <td>E</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>2.59</td>\n",
" <td>74.00</td>\n",
" <td>68</td>\n",
" <td>65</td>\n",
" <td>control</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210090</th>\n",
" <td>E</td>\n",
" <td>hematoma</td>\n",
" <td>4.08</td>\n",
" <td>68.00</td>\n",
" <td>50</td>\n",
" <td>72</td>\n",
" <td>not specified</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210188</th>\n",
" <td>E</td>\n",
" <td>metastatic non-small cell adenocarcinoma</td>\n",
" <td>1.20</td>\n",
" <td>72.00</td>\n",
" <td>65</td>\n",
" <td>63</td>\n",
" <td>not specified</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210192</th>\n",
" <td>E</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>2.31</td>\n",
" <td>75.00</td>\n",
" <td>50</td>\n",
" <td>65</td>\n",
" <td>control</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210193</th>\n",
" <td>E</td>\n",
" <td>Unknown</td>\n",
" <td>1.63</td>\n",
" <td>80.78</td>\n",
" <td>67</td>\n",
" <td>66</td>\n",
" <td>not specified</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210194</th>\n",
" <td>E</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" <td>0.52</td>\n",
" <td>58.00</td>\n",
" <td>56</td>\n",
" <td>60</td>\n",
" <td>chronic obstructive pulmonary disease</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210196</th>\n",
" <td>E</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>2.30</td>\n",
" <td>74.00</td>\n",
" <td>57</td>\n",
" <td>65</td>\n",
" <td>control</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210978</th>\n",
" <td>E</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>1.53</td>\n",
" <td>74.00</td>\n",
" <td>73</td>\n",
" <td>66</td>\n",
" <td>not specified</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210979</th>\n",
" <td>E</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>2.17</td>\n",
" <td>76.00</td>\n",
" <td>55</td>\n",
" <td>63</td>\n",
" <td>control</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210992</th>\n",
" <td>E</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" <td>0.90</td>\n",
" <td>55.90</td>\n",
" <td>70</td>\n",
" <td>71</td>\n",
" <td>chronic obstructive pulmonary disease</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210993</th>\n",
" <td>E</td>\n",
" <td>giant bullae</td>\n",
" <td>0.40</td>\n",
" <td>45.00</td>\n",
" <td>61</td>\n",
" <td>73</td>\n",
" <td>chronic obstructive pulmonary disease</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210994</th>\n",
" <td>E</td>\n",
" <td>carcinoid</td>\n",
" <td>1.69</td>\n",
" <td>76.00</td>\n",
" <td>64</td>\n",
" <td>63</td>\n",
" <td>not specified</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM211007</th>\n",
" <td>E</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" <td>1.70</td>\n",
" <td>59.00</td>\n",
" <td>61</td>\n",
" <td>66</td>\n",
" <td>chronic obstructive pulmonary disease</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM211008</th>\n",
" <td>E</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>3.66</td>\n",
" <td>72.00</td>\n",
" <td>71</td>\n",
" <td>71</td>\n",
" <td>control</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM211009</th>\n",
" <td>E</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>1.64</td>\n",
" <td>41.00</td>\n",
" <td>75</td>\n",
" <td>71</td>\n",
" <td>chronic obstructive pulmonary disease</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM211010</th>\n",
" <td>E</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>1.44</td>\n",
" <td>86.00</td>\n",
" <td>61</td>\n",
" <td>60</td>\n",
" <td>not specified</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM211865</th>\n",
" <td>E</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" <td>2.13</td>\n",
" <td>71.00</td>\n",
" <td>69</td>\n",
" <td>67</td>\n",
" <td>not specified</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM211872</th>\n",
" <td>E</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" <td>2.61</td>\n",
" <td>70.00</td>\n",
" <td>74</td>\n",
" <td>70</td>\n",
" <td>not specified</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212067</th>\n",
" <td>E</td>\n",
" <td>inflammation</td>\n",
" <td>4.04</td>\n",
" <td>79.00</td>\n",
" <td>55</td>\n",
" <td>69</td>\n",
" <td>control</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212068</th>\n",
" <td>E</td>\n",
" <td>metastatic renal cell carcinoma</td>\n",
" <td>1.99</td>\n",
" <td>85.00</td>\n",
" <td>78</td>\n",
" <td>63</td>\n",
" <td>control</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212069</th>\n",
" <td>E</td>\n",
" <td>no malignancy</td>\n",
" <td>1.60</td>\n",
" <td>77.00</td>\n",
" <td>81</td>\n",
" <td>66</td>\n",
" <td>not specified</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212070</th>\n",
" <td>E</td>\n",
" <td>carcinoid</td>\n",
" <td>3.70</td>\n",
" <td>81.86</td>\n",
" <td>40</td>\n",
" <td>67</td>\n",
" <td>control</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212074</th>\n",
" <td>E</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" <td>2.06</td>\n",
" <td>54.00</td>\n",
" <td>64</td>\n",
" <td>65</td>\n",
" <td>chronic obstructive pulmonary disease</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212075</th>\n",
" <td>E</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" <td>1.30</td>\n",
" <td>78.00</td>\n",
" <td>79</td>\n",
" <td>63</td>\n",
" <td>chronic obstructive pulmonary disease</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Afro American</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212787</th>\n",
" <td>E</td>\n",
" <td>NSC-Mixed</td>\n",
" <td>3.66</td>\n",
" <td>78.00</td>\n",
" <td>78</td>\n",
" <td>70</td>\n",
" <td>control</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212788</th>\n",
" <td>E</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" <td>1.29</td>\n",
" <td>53.00</td>\n",
" <td>77</td>\n",
" <td>67</td>\n",
" <td>chronic obstructive pulmonary disease</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212789</th>\n",
" <td>E</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" <td>1.94</td>\n",
" <td>86.00</td>\n",
" <td>62</td>\n",
" <td>62</td>\n",
" <td>control</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212790</th>\n",
" <td>E</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" <td>2.83</td>\n",
" <td>75.00</td>\n",
" <td>54</td>\n",
" <td>75</td>\n",
" <td>control</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212809</th>\n",
" <td>E</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>1.28</td>\n",
" <td>89.00</td>\n",
" <td>61</td>\n",
" <td>65</td>\n",
" <td>not specified</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212810</th>\n",
" <td>E</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" <td>0.88</td>\n",
" <td>52.00</td>\n",
" <td>52</td>\n",
" <td>66</td>\n",
" <td>chronic obstructive pulmonary disease</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212811</th>\n",
" <td>E</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" <td>1.37</td>\n",
" <td>82.00</td>\n",
" <td>77</td>\n",
" <td>58</td>\n",
" <td>control</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212848</th>\n",
" <td>E</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" <td>0.55</td>\n",
" <td>44.00</td>\n",
" <td>59</td>\n",
" <td>58</td>\n",
" <td>chronic obstructive pulmonary disease</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212849</th>\n",
" <td>E</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>2.73</td>\n",
" <td>80.00</td>\n",
" <td>39</td>\n",
" <td>73</td>\n",
" <td>not specified</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212850</th>\n",
" <td>E</td>\n",
" <td>carcinoid</td>\n",
" <td>2.32</td>\n",
" <td>76.00</td>\n",
" <td>71</td>\n",
" <td>69</td>\n",
" <td>not specified</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212852</th>\n",
" <td>E</td>\n",
" <td>Giant Cell Tumor</td>\n",
" <td>0.99</td>\n",
" <td>63.00</td>\n",
" <td>72</td>\n",
" <td>60</td>\n",
" <td>chronic obstructive pulmonary disease</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212853</th>\n",
" <td>E</td>\n",
" <td>lymphoma</td>\n",
" <td>2.42</td>\n",
" <td>80.00</td>\n",
" <td>71</td>\n",
" <td>66</td>\n",
" <td>control</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212854</th>\n",
" <td>E</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>2.26</td>\n",
" <td>83.00</td>\n",
" <td>64</td>\n",
" <td>66</td>\n",
" <td>not specified</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212855</th>\n",
" <td>E</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>2.43</td>\n",
" <td>69.00</td>\n",
" <td>73</td>\n",
" <td>68</td>\n",
" <td>not specified</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM213017</th>\n",
" <td>E</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>2.12</td>\n",
" <td>73.00</td>\n",
" <td>79</td>\n",
" <td>69</td>\n",
" <td>not specified</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM213018</th>\n",
" <td>E</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>2.34</td>\n",
" <td>81.00</td>\n",
" <td>82</td>\n",
" <td>68</td>\n",
" <td>not specified</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM213019</th>\n",
" <td>E</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>1.70</td>\n",
" <td>72.00</td>\n",
" <td>71</td>\n",
" <td>71</td>\n",
" <td>not specified</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM213020</th>\n",
" <td>E</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>0.67</td>\n",
" <td>42.00</td>\n",
" <td>75</td>\n",
" <td>63</td>\n",
" <td>chronic obstructive pulmonary disease</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM213034</th>\n",
" <td>E</td>\n",
" <td>non-small cell adenocarcinoma</td>\n",
" <td>2.56</td>\n",
" <td>61.00</td>\n",
" <td>70</td>\n",
" <td>69</td>\n",
" <td>not specified</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM213035</th>\n",
" <td>E</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" <td>3.11</td>\n",
" <td>73.00</td>\n",
" <td>67</td>\n",
" <td>71</td>\n",
" <td>control</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM213036</th>\n",
" <td>E</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" <td>2.68</td>\n",
" <td>71.00</td>\n",
" <td>59</td>\n",
" <td>69</td>\n",
" <td>control</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>female</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM213037</th>\n",
" <td>E</td>\n",
" <td>non-small cell squamous cell carcinoma</td>\n",
" <td>2.25</td>\n",
" <td>72.00</td>\n",
" <td>77</td>\n",
" <td>66</td>\n",
" <td>not specified</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Caucasian</td>\n",
" <td>male</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"label Biomarker Data\\GPL570 \\\n",
"subject.inTrialId \n",
"GSE8581GSM210004 None \n",
"GSE8581GSM210005 None \n",
"GSE8581GSM210006 None \n",
"GSE8581GSM210007 E \n",
"GSE8581GSM210008 E \n",
"GSE8581GSM210009 E \n",
"GSE8581GSM210010 E \n",
"GSE8581GSM210011 E \n",
"GSE8581GSM210012 E \n",
"GSE8581GSM210014 E \n",
"GSE8581GSM210015 E \n",
"GSE8581GSM210071 E \n",
"GSE8581GSM210087 E \n",
"GSE8581GSM210090 E \n",
"GSE8581GSM210188 E \n",
"GSE8581GSM210192 E \n",
"GSE8581GSM210193 E \n",
"GSE8581GSM210194 E \n",
"GSE8581GSM210196 E \n",
"GSE8581GSM210978 E \n",
"GSE8581GSM210979 E \n",
"GSE8581GSM210992 E \n",
"GSE8581GSM210993 E \n",
"GSE8581GSM210994 E \n",
"GSE8581GSM211007 E \n",
"GSE8581GSM211008 E \n",
"GSE8581GSM211009 E \n",
"GSE8581GSM211010 E \n",
"GSE8581GSM211865 E \n",
"GSE8581GSM211872 E \n",
"GSE8581GSM212067 E \n",
"GSE8581GSM212068 E \n",
"GSE8581GSM212069 E \n",
"GSE8581GSM212070 E \n",
"GSE8581GSM212074 E \n",
"GSE8581GSM212075 E \n",
"GSE8581GSM212787 E \n",
"GSE8581GSM212788 E \n",
"GSE8581GSM212789 E \n",
"GSE8581GSM212790 E \n",
"GSE8581GSM212809 E \n",
"GSE8581GSM212810 E \n",
"GSE8581GSM212811 E \n",
"GSE8581GSM212848 E \n",
"GSE8581GSM212849 E \n",
"GSE8581GSM212850 E \n",
"GSE8581GSM212852 E \n",
"GSE8581GSM212853 E \n",
"GSE8581GSM212854 E \n",
"GSE8581GSM212855 E \n",
"GSE8581GSM213017 E \n",
"GSE8581GSM213018 E \n",
"GSE8581GSM213019 E \n",
"GSE8581GSM213020 E \n",
"GSE8581GSM213034 E \n",
"GSE8581GSM213035 E \n",
"GSE8581GSM213036 E \n",
"GSE8581GSM213037 E \n",
"\n",
"label Endpoints\\Diagnosis Endpoints\\FEV1 \\\n",
"subject.inTrialId \n",
"GSE8581GSM210004 non-small cell squamous cell carcinoma 2.54 \n",
"GSE8581GSM210005 non-small cell adenocarcinoma 1.69 \n",
"GSE8581GSM210006 non-small cell adenocarcinoma 1.41 \n",
"GSE8581GSM210007 non-small cell adenocarcinoma 2.51 \n",
"GSE8581GSM210008 non-small cell adenocarcinoma 1.64 \n",
"GSE8581GSM210009 non-small cell squamous cell carcinoma 2.72 \n",
"GSE8581GSM210010 non-small cell adenocarcinoma 1.45 \n",
"GSE8581GSM210011 non-small cell squamous cell carcinoma 1.87 \n",
"GSE8581GSM210012 non-small cell adenocarcinoma 2.76 \n",
"GSE8581GSM210014 non-small cell adenocarcinoma 1.98 \n",
"GSE8581GSM210015 non-small cell adenocarcinoma 2.59 \n",
"GSE8581GSM210071 emphysema 1.16 \n",
"GSE8581GSM210087 non-small cell adenocarcinoma 2.59 \n",
"GSE8581GSM210090 hematoma 4.08 \n",
"GSE8581GSM210188 metastatic non-small cell adenocarcinoma 1.20 \n",
"GSE8581GSM210192 non-small cell adenocarcinoma 2.31 \n",
"GSE8581GSM210193 Unknown 1.63 \n",
"GSE8581GSM210194 non-small cell squamous cell carcinoma 0.52 \n",
"GSE8581GSM210196 non-small cell adenocarcinoma 2.30 \n",
"GSE8581GSM210978 non-small cell adenocarcinoma 1.53 \n",
"GSE8581GSM210979 non-small cell adenocarcinoma 2.17 \n",
"GSE8581GSM210992 non-small cell squamous cell carcinoma 0.90 \n",
"GSE8581GSM210993 giant bullae 0.40 \n",
"GSE8581GSM210994 carcinoid 1.69 \n",
"GSE8581GSM211007 non-small cell squamous cell carcinoma 1.70 \n",
"GSE8581GSM211008 non-small cell adenocarcinoma 3.66 \n",
"GSE8581GSM211009 non-small cell adenocarcinoma 1.64 \n",
"GSE8581GSM211010 non-small cell adenocarcinoma 1.44 \n",
"GSE8581GSM211865 non-small cell squamous cell carcinoma 2.13 \n",
"GSE8581GSM211872 non-small cell squamous cell carcinoma 2.61 \n",
"GSE8581GSM212067 inflammation 4.04 \n",
"GSE8581GSM212068 metastatic renal cell carcinoma 1.99 \n",
"GSE8581GSM212069 no malignancy 1.60 \n",
"GSE8581GSM212070 carcinoid 3.70 \n",
"GSE8581GSM212074 non-small cell squamous cell carcinoma 2.06 \n",
"GSE8581GSM212075 non-small cell squamous cell carcinoma 1.30 \n",
"GSE8581GSM212787 NSC-Mixed 3.66 \n",
"GSE8581GSM212788 non-small cell squamous cell carcinoma 1.29 \n",
"GSE8581GSM212789 non-small cell squamous cell carcinoma 1.94 \n",
"GSE8581GSM212790 non-small cell squamous cell carcinoma 2.83 \n",
"GSE8581GSM212809 non-small cell adenocarcinoma 1.28 \n",
"GSE8581GSM212810 non-small cell squamous cell carcinoma 0.88 \n",
"GSE8581GSM212811 non-small cell squamous cell carcinoma 1.37 \n",
"GSE8581GSM212848 non-small cell squamous cell carcinoma 0.55 \n",
"GSE8581GSM212849 non-small cell adenocarcinoma 2.73 \n",
"GSE8581GSM212850 carcinoid 2.32 \n",
"GSE8581GSM212852 Giant Cell Tumor 0.99 \n",
"GSE8581GSM212853 lymphoma 2.42 \n",
"GSE8581GSM212854 non-small cell adenocarcinoma 2.26 \n",
"GSE8581GSM212855 non-small cell adenocarcinoma 2.43 \n",
"GSE8581GSM213017 non-small cell adenocarcinoma 2.12 \n",
"GSE8581GSM213018 non-small cell adenocarcinoma 2.34 \n",
"GSE8581GSM213019 non-small cell adenocarcinoma 1.70 \n",
"GSE8581GSM213020 non-small cell adenocarcinoma 0.67 \n",
"GSE8581GSM213034 non-small cell adenocarcinoma 2.56 \n",
"GSE8581GSM213035 non-small cell squamous cell carcinoma 3.11 \n",
"GSE8581GSM213036 non-small cell squamous cell carcinoma 2.68 \n",
"GSE8581GSM213037 non-small cell squamous cell carcinoma 2.25 \n",
"\n",
"label Endpoints\\Forced Expiratory Volume Ratio Subjects\\Age \\\n",
"subject.inTrialId \n",
"GSE8581GSM210004 58.00 63 \n",
"GSE8581GSM210005 83.66 84 \n",
"GSE8581GSM210006 51.00 65 \n",
"GSE8581GSM210007 80.96 46 \n",
"GSE8581GSM210008 57.00 53 \n",
"GSE8581GSM210009 74.00 53 \n",
"GSE8581GSM210010 73.00 77 \n",
"GSE8581GSM210011 56.00 56 \n",
"GSE8581GSM210012 70.58 61 \n",
"GSE8581GSM210014 78.00 71 \n",
"GSE8581GSM210015 74.00 68 \n",
"GSE8581GSM210071 43.00 68 \n",
"GSE8581GSM210087 74.00 68 \n",
"GSE8581GSM210090 68.00 50 \n",
"GSE8581GSM210188 72.00 65 \n",
"GSE8581GSM210192 75.00 50 \n",
"GSE8581GSM210193 80.78 67 \n",
"GSE8581GSM210194 58.00 56 \n",
"GSE8581GSM210196 74.00 57 \n",
"GSE8581GSM210978 74.00 73 \n",
"GSE8581GSM210979 76.00 55 \n",
"GSE8581GSM210992 55.90 70 \n",
"GSE8581GSM210993 45.00 61 \n",
"GSE8581GSM210994 76.00 64 \n",
"GSE8581GSM211007 59.00 61 \n",
"GSE8581GSM211008 72.00 71 \n",
"GSE8581GSM211009 41.00 75 \n",
"GSE8581GSM211010 86.00 61 \n",
"GSE8581GSM211865 71.00 69 \n",
"GSE8581GSM211872 70.00 74 \n",
"GSE8581GSM212067 79.00 55 \n",
"GSE8581GSM212068 85.00 78 \n",
"GSE8581GSM212069 77.00 81 \n",
"GSE8581GSM212070 81.86 40 \n",
"GSE8581GSM212074 54.00 64 \n",
"GSE8581GSM212075 78.00 79 \n",
"GSE8581GSM212787 78.00 78 \n",
"GSE8581GSM212788 53.00 77 \n",
"GSE8581GSM212789 86.00 62 \n",
"GSE8581GSM212790 75.00 54 \n",
"GSE8581GSM212809 89.00 61 \n",
"GSE8581GSM212810 52.00 52 \n",
"GSE8581GSM212811 82.00 77 \n",
"GSE8581GSM212848 44.00 59 \n",
"GSE8581GSM212849 80.00 39 \n",
"GSE8581GSM212850 76.00 71 \n",
"GSE8581GSM212852 63.00 72 \n",
"GSE8581GSM212853 80.00 71 \n",
"GSE8581GSM212854 83.00 64 \n",
"GSE8581GSM212855 69.00 73 \n",
"GSE8581GSM213017 73.00 79 \n",
"GSE8581GSM213018 81.00 82 \n",
"GSE8581GSM213019 72.00 71 \n",
"GSE8581GSM213020 42.00 75 \n",
"GSE8581GSM213034 61.00 70 \n",
"GSE8581GSM213035 73.00 67 \n",
"GSE8581GSM213036 71.00 59 \n",
"GSE8581GSM213037 72.00 77 \n",
"\n",
"label Subjects\\Height (inch) \\\n",
"subject.inTrialId \n",
"GSE8581GSM210004 72 \n",
"GSE8581GSM210005 60 \n",
"GSE8581GSM210006 66 \n",
"GSE8581GSM210007 66 \n",
"GSE8581GSM210008 65 \n",
"GSE8581GSM210009 64 \n",
"GSE8581GSM210010 63 \n",
"GSE8581GSM210011 72 \n",
"GSE8581GSM210012 69 \n",
"GSE8581GSM210014 63 \n",
"GSE8581GSM210015 65 \n",
"GSE8581GSM210071 67 \n",
"GSE8581GSM210087 65 \n",
"GSE8581GSM210090 72 \n",
"GSE8581GSM210188 63 \n",
"GSE8581GSM210192 65 \n",
"GSE8581GSM210193 66 \n",
"GSE8581GSM210194 60 \n",
"GSE8581GSM210196 65 \n",
"GSE8581GSM210978 66 \n",
"GSE8581GSM210979 63 \n",
"GSE8581GSM210992 71 \n",
"GSE8581GSM210993 73 \n",
"GSE8581GSM210994 63 \n",
"GSE8581GSM211007 66 \n",
"GSE8581GSM211008 71 \n",
"GSE8581GSM211009 71 \n",
"GSE8581GSM211010 60 \n",
"GSE8581GSM211865 67 \n",
"GSE8581GSM211872 70 \n",
"GSE8581GSM212067 69 \n",
"GSE8581GSM212068 63 \n",
"GSE8581GSM212069 66 \n",
"GSE8581GSM212070 67 \n",
"GSE8581GSM212074 65 \n",
"GSE8581GSM212075 63 \n",
"GSE8581GSM212787 70 \n",
"GSE8581GSM212788 67 \n",
"GSE8581GSM212789 62 \n",
"GSE8581GSM212790 75 \n",
"GSE8581GSM212809 65 \n",
"GSE8581GSM212810 66 \n",
"GSE8581GSM212811 58 \n",
"GSE8581GSM212848 58 \n",
"GSE8581GSM212849 73 \n",
"GSE8581GSM212850 69 \n",
"GSE8581GSM212852 60 \n",
"GSE8581GSM212853 66 \n",
"GSE8581GSM212854 66 \n",
"GSE8581GSM212855 68 \n",
"GSE8581GSM213017 69 \n",
"GSE8581GSM213018 68 \n",
"GSE8581GSM213019 71 \n",
"GSE8581GSM213020 63 \n",
"GSE8581GSM213034 69 \n",
"GSE8581GSM213035 71 \n",
"GSE8581GSM213036 69 \n",
"GSE8581GSM213037 66 \n",
"\n",
"label Subjects\\Lung Disease Subjects\\Organism \\\n",
"subject.inTrialId \n",
"GSE8581GSM210004 chronic obstructive pulmonary disease Homo sapiens \n",
"GSE8581GSM210005 control Homo sapiens \n",
"GSE8581GSM210006 chronic obstructive pulmonary disease Homo sapiens \n",
"GSE8581GSM210007 not specified Homo sapiens \n",
"GSE8581GSM210008 chronic obstructive pulmonary disease Homo sapiens \n",
"GSE8581GSM210009 control Homo sapiens \n",
"GSE8581GSM210010 not specified Homo sapiens \n",
"GSE8581GSM210011 chronic obstructive pulmonary disease Homo sapiens \n",
"GSE8581GSM210012 not specified Homo sapiens \n",
"GSE8581GSM210014 control Homo sapiens \n",
"GSE8581GSM210015 control Homo sapiens \n",
"GSE8581GSM210071 chronic obstructive pulmonary disease Homo sapiens \n",
"GSE8581GSM210087 control Homo sapiens \n",
"GSE8581GSM210090 not specified Homo sapiens \n",
"GSE8581GSM210188 not specified Homo sapiens \n",
"GSE8581GSM210192 control Homo sapiens \n",
"GSE8581GSM210193 not specified Homo sapiens \n",
"GSE8581GSM210194 chronic obstructive pulmonary disease Homo sapiens \n",
"GSE8581GSM210196 control Homo sapiens \n",
"GSE8581GSM210978 not specified Homo sapiens \n",
"GSE8581GSM210979 control Homo sapiens \n",
"GSE8581GSM210992 chronic obstructive pulmonary disease Homo sapiens \n",
"GSE8581GSM210993 chronic obstructive pulmonary disease Homo sapiens \n",
"GSE8581GSM210994 not specified Homo sapiens \n",
"GSE8581GSM211007 chronic obstructive pulmonary disease Homo sapiens \n",
"GSE8581GSM211008 control Homo sapiens \n",
"GSE8581GSM211009 chronic obstructive pulmonary disease Homo sapiens \n",
"GSE8581GSM211010 not specified Homo sapiens \n",
"GSE8581GSM211865 not specified Homo sapiens \n",
"GSE8581GSM211872 not specified Homo sapiens \n",
"GSE8581GSM212067 control Homo sapiens \n",
"GSE8581GSM212068 control Homo sapiens \n",
"GSE8581GSM212069 not specified Homo sapiens \n",
"GSE8581GSM212070 control Homo sapiens \n",
"GSE8581GSM212074 chronic obstructive pulmonary disease Homo sapiens \n",
"GSE8581GSM212075 chronic obstructive pulmonary disease Homo sapiens \n",
"GSE8581GSM212787 control Homo sapiens \n",
"GSE8581GSM212788 chronic obstructive pulmonary disease Homo sapiens \n",
"GSE8581GSM212789 control Homo sapiens \n",
"GSE8581GSM212790 control Homo sapiens \n",
"GSE8581GSM212809 not specified Homo sapiens \n",
"GSE8581GSM212810 chronic obstructive pulmonary disease Homo sapiens \n",
"GSE8581GSM212811 control Homo sapiens \n",
"GSE8581GSM212848 chronic obstructive pulmonary disease Homo sapiens \n",
"GSE8581GSM212849 not specified Homo sapiens \n",
"GSE8581GSM212850 not specified Homo sapiens \n",
"GSE8581GSM212852 chronic obstructive pulmonary disease Homo sapiens \n",
"GSE8581GSM212853 control Homo sapiens \n",
"GSE8581GSM212854 not specified Homo sapiens \n",
"GSE8581GSM212855 not specified Homo sapiens \n",
"GSE8581GSM213017 not specified Homo sapiens \n",
"GSE8581GSM213018 not specified Homo sapiens \n",
"GSE8581GSM213019 not specified Homo sapiens \n",
"GSE8581GSM213020 chronic obstructive pulmonary disease Homo sapiens \n",
"GSE8581GSM213034 not specified Homo sapiens \n",
"GSE8581GSM213035 control Homo sapiens \n",
"GSE8581GSM213036 control Homo sapiens \n",
"GSE8581GSM213037 not specified Homo sapiens \n",
"\n",
"label Subjects\\Race Subjects\\Sex \n",
"subject.inTrialId \n",
"GSE8581GSM210004 Caucasian male \n",
"GSE8581GSM210005 Afro American female \n",
"GSE8581GSM210006 Afro American female \n",
"GSE8581GSM210007 Caucasian male \n",
"GSE8581GSM210008 Caucasian female \n",
"GSE8581GSM210009 Caucasian female \n",
"GSE8581GSM210010 Caucasian female \n",
"GSE8581GSM210011 Caucasian male \n",
"GSE8581GSM210012 Caucasian male \n",
"GSE8581GSM210014 Caucasian female \n",
"GSE8581GSM210015 Caucasian male \n",
"GSE8581GSM210071 Caucasian male \n",
"GSE8581GSM210087 Caucasian female \n",
"GSE8581GSM210090 Caucasian male \n",
"GSE8581GSM210188 Caucasian female \n",
"GSE8581GSM210192 Caucasian female \n",
"GSE8581GSM210193 Caucasian female \n",
"GSE8581GSM210194 Caucasian female \n",
"GSE8581GSM210196 Caucasian female \n",
"GSE8581GSM210978 Caucasian female \n",
"GSE8581GSM210979 Caucasian female \n",
"GSE8581GSM210992 Caucasian male \n",
"GSE8581GSM210993 Caucasian male \n",
"GSE8581GSM210994 Caucasian female \n",
"GSE8581GSM211007 Caucasian male \n",
"GSE8581GSM211008 Caucasian male \n",
"GSE8581GSM211009 Caucasian male \n",
"GSE8581GSM211010 Caucasian female \n",
"GSE8581GSM211865 Caucasian male \n",
"GSE8581GSM211872 Caucasian male \n",
"GSE8581GSM212067 Caucasian male \n",
"GSE8581GSM212068 Caucasian female \n",
"GSE8581GSM212069 Caucasian female \n",
"GSE8581GSM212070 Caucasian male \n",
"GSE8581GSM212074 Caucasian male \n",
"GSE8581GSM212075 Afro American female \n",
"GSE8581GSM212787 Caucasian male \n",
"GSE8581GSM212788 Caucasian female \n",
"GSE8581GSM212789 Caucasian female \n",
"GSE8581GSM212790 Caucasian female \n",
"GSE8581GSM212809 Caucasian female \n",
"GSE8581GSM212810 Caucasian female \n",
"GSE8581GSM212811 Caucasian female \n",
"GSE8581GSM212848 Caucasian female \n",
"GSE8581GSM212849 Caucasian male \n",
"GSE8581GSM212850 Caucasian male \n",
"GSE8581GSM212852 Caucasian female \n",
"GSE8581GSM212853 Caucasian female \n",
"GSE8581GSM212854 Caucasian male \n",
"GSE8581GSM212855 Caucasian male \n",
"GSE8581GSM213017 Caucasian male \n",
"GSE8581GSM213018 Caucasian male \n",
"GSE8581GSM213019 Caucasian female \n",
"GSE8581GSM213020 Caucasian male \n",
"GSE8581GSM213034 Caucasian male \n",
"GSE8581GSM213035 Caucasian male \n",
"GSE8581GSM213036 Caucasian female \n",
"GSE8581GSM213037 Caucasian male "
]
},
"execution_count": 30,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"obs_df2 = obs_df1.pivot(index = 'subject.inTrialId', columns = 'label', values = 'value')\n",
"obs_df3 = obs_df2.convert_objects()\n",
"obs_df4 = obs_df3.rename(\n",
" columns = lambda c: c.replace('\\Public Studies\\GSE8581\\\\', '')[:-1],\n",
" inplace = False)\n",
"obs_df4"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Split the **control** and **chronic obstructive pulmonary disease** sets:"
]
},
{
"cell_type": "code",
"execution_count": 31,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"control = obs_df4['Subjects\\Lung Disease'] == 'control'\n",
"treatment = obs_df4['Subjects\\Lung Disease'] == 'chronic obstructive pulmonary disease'"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Some basic statistics comparing the numerical attributes of both sets:"
]
},
{
"cell_type": "code",
"execution_count": 32,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>Endpoints\\FEV1</th>\n",
" <th>Endpoints\\Forced Expiratory Volume Ratio</th>\n",
" <th>Subjects\\Age</th>\n",
" <th>Subjects\\Height (inch)</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>count</th>\n",
" <td>19.000000</td>\n",
" <td>19.000000</td>\n",
" <td>19.000000</td>\n",
" <td>19.000000</td>\n",
" </tr>\n",
" <tr>\n",
" <th>mean</th>\n",
" <td>2.618421</td>\n",
" <td>77.448421</td>\n",
" <td>64.105263</td>\n",
" <td>65.842105</td>\n",
" </tr>\n",
" <tr>\n",
" <th>std</th>\n",
" <td>0.737219</td>\n",
" <td>4.540892</td>\n",
" <td>11.503114</td>\n",
" <td>4.193423</td>\n",
" </tr>\n",
" <tr>\n",
" <th>min</th>\n",
" <td>1.370000</td>\n",
" <td>71.000000</td>\n",
" <td>40.000000</td>\n",
" <td>58.000000</td>\n",
" </tr>\n",
" <tr>\n",
" <th>25%</th>\n",
" <td>2.080000</td>\n",
" <td>74.000000</td>\n",
" <td>55.000000</td>\n",
" <td>63.000000</td>\n",
" </tr>\n",
" <tr>\n",
" <th>50%</th>\n",
" <td>2.590000</td>\n",
" <td>76.000000</td>\n",
" <td>67.000000</td>\n",
" <td>65.000000</td>\n",
" </tr>\n",
" <tr>\n",
" <th>75%</th>\n",
" <td>2.970000</td>\n",
" <td>80.930000</td>\n",
" <td>71.000000</td>\n",
" <td>69.000000</td>\n",
" </tr>\n",
" <tr>\n",
" <th>max</th>\n",
" <td>4.040000</td>\n",
" <td>86.000000</td>\n",
" <td>84.000000</td>\n",
" <td>75.000000</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" Endpoints\\FEV1 Endpoints\\Forced Expiratory Volume Ratio Subjects\\Age \\\n",
"count 19.000000 19.000000 19.000000 \n",
"mean 2.618421 77.448421 64.105263 \n",
"std 0.737219 4.540892 11.503114 \n",
"min 1.370000 71.000000 40.000000 \n",
"25% 2.080000 74.000000 55.000000 \n",
"50% 2.590000 76.000000 67.000000 \n",
"75% 2.970000 80.930000 71.000000 \n",
"max 4.040000 86.000000 84.000000 \n",
"\n",
" Subjects\\Height (inch) \n",
"count 19.000000 \n",
"mean 65.842105 \n",
"std 4.193423 \n",
"min 58.000000 \n",
"25% 63.000000 \n",
"50% 65.000000 \n",
"75% 69.000000 \n",
"max 75.000000 "
]
},
"execution_count": 32,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"obs_df4[control].describe()"
]
},
{
"cell_type": "code",
"execution_count": 33,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>Endpoints\\FEV1</th>\n",
" <th>Endpoints\\Forced Expiratory Volume Ratio</th>\n",
" <th>Subjects\\Age</th>\n",
" <th>Subjects\\Height (inch)</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>count</th>\n",
" <td>17.000000</td>\n",
" <td>17.000000</td>\n",
" <td>17.000000</td>\n",
" <td>17.000000</td>\n",
" </tr>\n",
" <tr>\n",
" <th>mean</th>\n",
" <td>1.265882</td>\n",
" <td>53.523529</td>\n",
" <td>65.058824</td>\n",
" <td>66.176471</td>\n",
" </tr>\n",
" <tr>\n",
" <th>std</th>\n",
" <td>0.594433</td>\n",
" <td>9.205130</td>\n",
" <td>8.554754</td>\n",
" <td>4.530939</td>\n",
" </tr>\n",
" <tr>\n",
" <th>min</th>\n",
" <td>0.400000</td>\n",
" <td>41.000000</td>\n",
" <td>52.000000</td>\n",
" <td>58.000000</td>\n",
" </tr>\n",
" <tr>\n",
" <th>25%</th>\n",
" <td>0.880000</td>\n",
" <td>45.000000</td>\n",
" <td>59.000000</td>\n",
" <td>63.000000</td>\n",
" </tr>\n",
" <tr>\n",
" <th>50%</th>\n",
" <td>1.290000</td>\n",
" <td>54.000000</td>\n",
" <td>64.000000</td>\n",
" <td>66.000000</td>\n",
" </tr>\n",
" <tr>\n",
" <th>75%</th>\n",
" <td>1.640000</td>\n",
" <td>58.000000</td>\n",
" <td>72.000000</td>\n",
" <td>71.000000</td>\n",
" </tr>\n",
" <tr>\n",
" <th>max</th>\n",
" <td>2.540000</td>\n",
" <td>78.000000</td>\n",
" <td>79.000000</td>\n",
" <td>73.000000</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" Endpoints\\FEV1 Endpoints\\Forced Expiratory Volume Ratio Subjects\\Age \\\n",
"count 17.000000 17.000000 17.000000 \n",
"mean 1.265882 53.523529 65.058824 \n",
"std 0.594433 9.205130 8.554754 \n",
"min 0.400000 41.000000 52.000000 \n",
"25% 0.880000 45.000000 59.000000 \n",
"50% 1.290000 54.000000 64.000000 \n",
"75% 1.640000 58.000000 72.000000 \n",
"max 2.540000 78.000000 79.000000 \n",
"\n",
" Subjects\\Height (inch) \n",
"count 17.000000 \n",
"mean 66.176471 \n",
"std 4.530939 \n",
"min 58.000000 \n",
"25% 63.000000 \n",
"50% 66.000000 \n",
"75% 71.000000 \n",
"max 73.000000 "
]
},
"execution_count": 33,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"obs_df4[treatment].describe()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Part 2 - Retrieving molecular (aka \"high dimensional\") data\n",
"------------------\n",
"\n",
"\n",
"## Downloading the expression data for our chosen study\n",
"\n",
"This can take a while (~1 minute)"
]
},
{
"cell_type": "code",
"execution_count": 41,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"(hdHeader, hdRows) = api.get_hd_node_data(study = study_id,\n",
" node_name = 'Lung',\n",
" projection='log_intensity')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Select only the data rows where the probes are mapped to a gene (aka bioMarker). Gene ID\\probe ID will form the row names while the patientId values are used for the columns."
]
},
{
"cell_type": "code",
"execution_count": 42,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"rows = [row.value[0].doubleValue._values for row in hdRows if row.bioMarker != 'null']\n",
"row_names = [row.bioMarker + \"\\\\\" + row.label for row in hdRows if row.bioMarker != 'null']\n",
"col_names = [assay.patientId for assay in hdHeader.assay]"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Build the table as a DataFrame in Pandas:"
]
},
{
"cell_type": "code",
"execution_count": 43,
"metadata": {
"collapsed": false,
"scrolled": true
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>GSE8581GSM213034</th>\n",
" <th>GSE8581GSM212811</th>\n",
" <th>GSE8581GSM213036</th>\n",
" <th>GSE8581GSM212075</th>\n",
" <th>GSE8581GSM211008</th>\n",
" <th>GSE8581GSM210090</th>\n",
" <th>GSE8581GSM212855</th>\n",
" <th>GSE8581GSM212070</th>\n",
" <th>GSE8581GSM212810</th>\n",
" <th>GSE8581GSM210193</th>\n",
" <th>...</th>\n",
" <th>GSE8581GSM210979</th>\n",
" <th>GSE8581GSM213017</th>\n",
" <th>GSE8581GSM211007</th>\n",
" <th>GSE8581GSM210192</th>\n",
" <th>GSE8581GSM213020</th>\n",
" <th>GSE8581GSM210994</th>\n",
" <th>GSE8581GSM210010</th>\n",
" <th>GSE8581GSM210011</th>\n",
" <th>GSE8581GSM210007</th>\n",
" <th>GSE8581GSM213019</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>KIAA1377\\235956_at</th>\n",
" <td>6.461792</td>\n",
" <td>7.461758</td>\n",
" <td>6.907191</td>\n",
" <td>7.775558</td>\n",
" <td>7.308785</td>\n",
" <td>6.286654</td>\n",
" <td>4.924318</td>\n",
" <td>8.004900</td>\n",
" <td>2.411315</td>\n",
" <td>6.670685</td>\n",
" <td>...</td>\n",
" <td>7.888354</td>\n",
" <td>6.538960</td>\n",
" <td>7.314416</td>\n",
" <td>5.892823</td>\n",
" <td>6.554481</td>\n",
" <td>7.427330</td>\n",
" <td>5.623677</td>\n",
" <td>5.559804</td>\n",
" <td>6.104142</td>\n",
" <td>6.969680</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ZNF358\\226260_x_at</th>\n",
" <td>4.969012</td>\n",
" <td>1.053695</td>\n",
" <td>5.064348</td>\n",
" <td>4.766791</td>\n",
" <td>3.559235</td>\n",
" <td>4.967538</td>\n",
" <td>4.085595</td>\n",
" <td>4.767745</td>\n",
" <td>-1.447194</td>\n",
" <td>4.025853</td>\n",
" <td>...</td>\n",
" <td>4.780016</td>\n",
" <td>4.606946</td>\n",
" <td>5.232454</td>\n",
" <td>4.568361</td>\n",
" <td>4.537433</td>\n",
" <td>3.196739</td>\n",
" <td>3.986893</td>\n",
" <td>4.851469</td>\n",
" <td>3.962614</td>\n",
" <td>5.654816</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GPR135\\214503_x_at</th>\n",
" <td>0.313037</td>\n",
" <td>-1.114216</td>\n",
" <td>0.569997</td>\n",
" <td>-0.156695</td>\n",
" <td>0.268782</td>\n",
" <td>0.108009</td>\n",
" <td>1.087890</td>\n",
" <td>1.194270</td>\n",
" <td>-1.321647</td>\n",
" <td>0.938911</td>\n",
" <td>...</td>\n",
" <td>0.686541</td>\n",
" <td>0.696047</td>\n",
" <td>1.137484</td>\n",
" <td>0.213963</td>\n",
" <td>0.964066</td>\n",
" <td>-0.252259</td>\n",
" <td>0.214336</td>\n",
" <td>0.566046</td>\n",
" <td>0.067900</td>\n",
" <td>-0.266347</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GPATCH2\\242224_at</th>\n",
" <td>4.989094</td>\n",
" <td>4.451818</td>\n",
" <td>4.066089</td>\n",
" <td>4.839037</td>\n",
" <td>4.612494</td>\n",
" <td>4.843898</td>\n",
" <td>3.584397</td>\n",
" <td>5.486096</td>\n",
" <td>-1.439762</td>\n",
" <td>5.385900</td>\n",
" <td>...</td>\n",
" <td>5.263271</td>\n",
" <td>3.356482</td>\n",
" <td>5.831609</td>\n",
" <td>4.992265</td>\n",
" <td>5.039222</td>\n",
" <td>5.572077</td>\n",
" <td>4.678433</td>\n",
" <td>4.641962</td>\n",
" <td>4.997518</td>\n",
" <td>5.041904</td>\n",
" </tr>\n",
" <tr>\n",
" <th>RPL24\\214143_x_at</th>\n",
" <td>12.746451</td>\n",
" <td>12.414838</td>\n",
" <td>12.393632</td>\n",
" <td>12.335932</td>\n",
" <td>12.488262</td>\n",
" <td>12.386385</td>\n",
" <td>12.630738</td>\n",
" <td>12.627675</td>\n",
" <td>-1.703159</td>\n",
" <td>12.229774</td>\n",
" <td>...</td>\n",
" <td>12.501332</td>\n",
" <td>12.276255</td>\n",
" <td>12.471353</td>\n",
" <td>12.024201</td>\n",
" <td>12.642733</td>\n",
" <td>12.585993</td>\n",
" <td>12.109086</td>\n",
" <td>11.953891</td>\n",
" <td>11.624786</td>\n",
" <td>13.002877</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PALM2\\1554640_at</th>\n",
" <td>4.713311</td>\n",
" <td>4.580507</td>\n",
" <td>4.187253</td>\n",
" <td>5.226393</td>\n",
" <td>2.517850</td>\n",
" <td>3.331075</td>\n",
" <td>6.681140</td>\n",
" <td>6.004290</td>\n",
" <td>2.274962</td>\n",
" <td>4.748209</td>\n",
" <td>...</td>\n",
" <td>5.663384</td>\n",
" <td>5.626687</td>\n",
" <td>6.290896</td>\n",
" <td>4.591548</td>\n",
" <td>5.503263</td>\n",
" <td>5.310369</td>\n",
" <td>4.924789</td>\n",
" <td>5.146977</td>\n",
" <td>5.019933</td>\n",
" <td>5.911052</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC339316\\242084_at</th>\n",
" <td>0.759616</td>\n",
" <td>0.678216</td>\n",
" <td>3.717528</td>\n",
" <td>-0.063451</td>\n",
" <td>2.928876</td>\n",
" <td>0.940558</td>\n",
" <td>1.084091</td>\n",
" <td>1.457789</td>\n",
" <td>2.189900</td>\n",
" <td>-0.265294</td>\n",
" <td>...</td>\n",
" <td>1.123342</td>\n",
" <td>0.006305</td>\n",
" <td>4.473248</td>\n",
" <td>-0.392482</td>\n",
" <td>0.871686</td>\n",
" <td>1.391069</td>\n",
" <td>-0.194356</td>\n",
" <td>0.083697</td>\n",
" <td>3.514753</td>\n",
" <td>1.218781</td>\n",
" </tr>\n",
" <tr>\n",
" <th>FECH\\203115_at</th>\n",
" <td>5.924822</td>\n",
" <td>5.616725</td>\n",
" <td>4.892148</td>\n",
" <td>5.171583</td>\n",
" <td>5.930726</td>\n",
" <td>5.670852</td>\n",
" <td>4.090447</td>\n",
" <td>6.350764</td>\n",
" <td>-1.860861</td>\n",
" <td>5.720448</td>\n",
" <td>...</td>\n",
" <td>6.834496</td>\n",
" <td>5.207846</td>\n",
" <td>5.843306</td>\n",
" <td>5.312484</td>\n",
" <td>4.892386</td>\n",
" <td>5.718230</td>\n",
" <td>5.333832</td>\n",
" <td>4.882795</td>\n",
" <td>5.789813</td>\n",
" <td>6.214107</td>\n",
" </tr>\n",
" <tr>\n",
" <th>KCNJ9\\207527_at</th>\n",
" <td>3.415177</td>\n",
" <td>2.037192</td>\n",
" <td>3.383345</td>\n",
" <td>3.765651</td>\n",
" <td>3.043836</td>\n",
" <td>4.304745</td>\n",
" <td>2.253039</td>\n",
" <td>3.360196</td>\n",
" <td>-1.547046</td>\n",
" <td>4.613791</td>\n",
" <td>...</td>\n",
" <td>4.069548</td>\n",
" <td>3.205654</td>\n",
" <td>3.604522</td>\n",
" <td>2.567180</td>\n",
" <td>3.076275</td>\n",
" <td>3.840896</td>\n",
" <td>3.597162</td>\n",
" <td>1.285207</td>\n",
" <td>1.642979</td>\n",
" <td>4.039182</td>\n",
" </tr>\n",
" <tr>\n",
" <th>C21orf96\\220918_at</th>\n",
" <td>5.862719</td>\n",
" <td>5.615584</td>\n",
" <td>6.010954</td>\n",
" <td>6.295001</td>\n",
" <td>4.157214</td>\n",
" <td>4.917064</td>\n",
" <td>4.885101</td>\n",
" <td>5.563570</td>\n",
" <td>2.084779</td>\n",
" <td>5.801756</td>\n",
" <td>...</td>\n",
" <td>5.384008</td>\n",
" <td>3.163640</td>\n",
" <td>5.905125</td>\n",
" <td>4.462373</td>\n",
" <td>5.391685</td>\n",
" <td>4.537215</td>\n",
" <td>5.284943</td>\n",
" <td>4.878632</td>\n",
" <td>4.544145</td>\n",
" <td>6.354914</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SAT2\\225272_at</th>\n",
" <td>8.531444</td>\n",
" <td>8.361009</td>\n",
" <td>8.189889</td>\n",
" <td>8.728519</td>\n",
" <td>7.830052</td>\n",
" <td>8.680068</td>\n",
" <td>7.434945</td>\n",
" <td>8.948992</td>\n",
" <td>1.320987</td>\n",
" <td>7.738741</td>\n",
" <td>...</td>\n",
" <td>7.510827</td>\n",
" <td>7.241602</td>\n",
" <td>7.443913</td>\n",
" <td>8.204175</td>\n",
" <td>7.967803</td>\n",
" <td>7.214970</td>\n",
" <td>8.177086</td>\n",
" <td>7.745654</td>\n",
" <td>7.629014</td>\n",
" <td>8.572253</td>\n",
" </tr>\n",
" <tr>\n",
" <th>EHD1\\209038_s_at</th>\n",
" <td>4.654092</td>\n",
" <td>5.696230</td>\n",
" <td>5.233359</td>\n",
" <td>5.462065</td>\n",
" <td>4.909850</td>\n",
" <td>5.028790</td>\n",
" <td>5.613700</td>\n",
" <td>6.709029</td>\n",
" <td>0.626093</td>\n",
" <td>4.729270</td>\n",
" <td>...</td>\n",
" <td>5.031285</td>\n",
" <td>3.642690</td>\n",
" <td>2.643683</td>\n",
" <td>4.169444</td>\n",
" <td>5.328567</td>\n",
" <td>1.194219</td>\n",
" <td>3.985938</td>\n",
" <td>4.281810</td>\n",
" <td>4.666552</td>\n",
" <td>5.242256</td>\n",
" </tr>\n",
" <tr>\n",
" <th>CBLB\\208348_s_at</th>\n",
" <td>2.811568</td>\n",
" <td>-1.355841</td>\n",
" <td>1.747310</td>\n",
" <td>2.343664</td>\n",
" <td>3.683607</td>\n",
" <td>-0.044488</td>\n",
" <td>0.603587</td>\n",
" <td>2.026049</td>\n",
" <td>0.551934</td>\n",
" <td>3.633629</td>\n",
" <td>...</td>\n",
" <td>4.673251</td>\n",
" <td>2.894183</td>\n",
" <td>1.403611</td>\n",
" <td>2.498493</td>\n",
" <td>0.506145</td>\n",
" <td>1.890999</td>\n",
" <td>0.135535</td>\n",
" <td>2.395208</td>\n",
" <td>3.197502</td>\n",
" <td>0.186754</td>\n",
" </tr>\n",
" <tr>\n",
" <th>C20orf85\\229542_at</th>\n",
" <td>6.652214</td>\n",
" <td>7.913548</td>\n",
" <td>7.191395</td>\n",
" <td>8.238376</td>\n",
" <td>5.263647</td>\n",
" <td>6.728356</td>\n",
" <td>3.488888</td>\n",
" <td>8.462748</td>\n",
" <td>1.447971</td>\n",
" <td>6.153043</td>\n",
" <td>...</td>\n",
" <td>6.658311</td>\n",
" <td>6.841860</td>\n",
" <td>6.844750</td>\n",
" <td>5.872060</td>\n",
" <td>7.208459</td>\n",
" <td>6.531349</td>\n",
" <td>3.587077</td>\n",
" <td>6.786636</td>\n",
" <td>6.914182</td>\n",
" <td>5.792871</td>\n",
" </tr>\n",
" <tr>\n",
" <th>UGGT1\\218257_s_at</th>\n",
" <td>5.788636</td>\n",
" <td>5.553766</td>\n",
" <td>5.148186</td>\n",
" <td>6.058695</td>\n",
" <td>5.965759</td>\n",
" <td>6.196871</td>\n",
" <td>5.516945</td>\n",
" <td>6.552457</td>\n",
" <td>1.104357</td>\n",
" <td>6.008482</td>\n",
" <td>...</td>\n",
" <td>6.032028</td>\n",
" <td>4.263155</td>\n",
" <td>5.904243</td>\n",
" <td>5.303737</td>\n",
" <td>5.705884</td>\n",
" <td>5.735067</td>\n",
" <td>5.761126</td>\n",
" <td>5.646946</td>\n",
" <td>5.580655</td>\n",
" <td>5.697907</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC283585\\1561442_at</th>\n",
" <td>2.861265</td>\n",
" <td>2.867798</td>\n",
" <td>4.049178</td>\n",
" <td>1.020051</td>\n",
" <td>4.728040</td>\n",
" <td>4.182049</td>\n",
" <td>3.484486</td>\n",
" <td>3.133233</td>\n",
" <td>0.538767</td>\n",
" <td>3.861102</td>\n",
" <td>...</td>\n",
" <td>3.705093</td>\n",
" <td>1.710636</td>\n",
" <td>4.286031</td>\n",
" <td>2.594986</td>\n",
" <td>4.520120</td>\n",
" <td>4.288447</td>\n",
" <td>3.505434</td>\n",
" <td>4.012971</td>\n",
" <td>3.750939</td>\n",
" <td>4.374720</td>\n",
" </tr>\n",
" <tr>\n",
" <th>EMP2\\204975_at</th>\n",
" <td>11.154514</td>\n",
" <td>10.251210</td>\n",
" <td>10.557148</td>\n",
" <td>11.385383</td>\n",
" <td>11.230987</td>\n",
" <td>11.683977</td>\n",
" <td>10.720920</td>\n",
" <td>12.007297</td>\n",
" <td>-1.408148</td>\n",
" <td>10.843474</td>\n",
" <td>...</td>\n",
" <td>11.797297</td>\n",
" <td>11.277770</td>\n",
" <td>11.592742</td>\n",
" <td>10.794018</td>\n",
" <td>11.989767</td>\n",
" <td>11.484546</td>\n",
" <td>10.659693</td>\n",
" <td>10.273108</td>\n",
" <td>10.974938</td>\n",
" <td>11.568312</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LHFP\\218656_s_at</th>\n",
" <td>9.192811</td>\n",
" <td>9.300302</td>\n",
" <td>9.506220</td>\n",
" <td>9.353908</td>\n",
" <td>9.686849</td>\n",
" <td>9.403093</td>\n",
" <td>9.158880</td>\n",
" <td>10.142222</td>\n",
" <td>0.891201</td>\n",
" <td>10.167130</td>\n",
" <td>...</td>\n",
" <td>10.192170</td>\n",
" <td>9.059190</td>\n",
" <td>9.559033</td>\n",
" <td>9.442676</td>\n",
" <td>9.684657</td>\n",
" <td>9.931885</td>\n",
" <td>9.438902</td>\n",
" <td>8.614493</td>\n",
" <td>9.072494</td>\n",
" <td>9.847826</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SNCAIP\\237834_at</th>\n",
" <td>3.468440</td>\n",
" <td>1.408119</td>\n",
" <td>3.229285</td>\n",
" <td>2.280220</td>\n",
" <td>2.810227</td>\n",
" <td>2.852077</td>\n",
" <td>2.748893</td>\n",
" <td>1.926686</td>\n",
" <td>2.686270</td>\n",
" <td>2.555478</td>\n",
" <td>...</td>\n",
" <td>3.470042</td>\n",
" <td>-0.904038</td>\n",
" <td>4.527971</td>\n",
" <td>3.324350</td>\n",
" <td>3.490403</td>\n",
" <td>0.654142</td>\n",
" <td>2.098797</td>\n",
" <td>1.903358</td>\n",
" <td>3.349436</td>\n",
" <td>1.955607</td>\n",
" </tr>\n",
" <tr>\n",
" <th>RDH8\\220683_at</th>\n",
" <td>3.984535</td>\n",
" <td>4.318512</td>\n",
" <td>0.107701</td>\n",
" <td>4.391073</td>\n",
" <td>3.984945</td>\n",
" <td>4.485176</td>\n",
" <td>2.713984</td>\n",
" <td>4.919788</td>\n",
" <td>-0.327627</td>\n",
" <td>4.501879</td>\n",
" <td>...</td>\n",
" <td>3.168956</td>\n",
" <td>1.150722</td>\n",
" <td>5.495113</td>\n",
" <td>4.482984</td>\n",
" <td>4.278468</td>\n",
" <td>5.238550</td>\n",
" <td>2.795484</td>\n",
" <td>2.430928</td>\n",
" <td>4.177711</td>\n",
" <td>4.846423</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SRSF4\\239512_at</th>\n",
" <td>7.591979</td>\n",
" <td>5.857429</td>\n",
" <td>7.502020</td>\n",
" <td>8.401899</td>\n",
" <td>8.216115</td>\n",
" <td>7.893508</td>\n",
" <td>7.413916</td>\n",
" <td>8.478094</td>\n",
" <td>1.221227</td>\n",
" <td>7.565925</td>\n",
" <td>...</td>\n",
" <td>8.778008</td>\n",
" <td>6.416321</td>\n",
" <td>8.609762</td>\n",
" <td>7.581886</td>\n",
" <td>8.321924</td>\n",
" <td>8.600660</td>\n",
" <td>7.747475</td>\n",
" <td>7.589434</td>\n",
" <td>8.392601</td>\n",
" <td>8.622656</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ACTB\\213867_x_at</th>\n",
" <td>13.404822</td>\n",
" <td>12.845100</td>\n",
" <td>13.204111</td>\n",
" <td>13.159971</td>\n",
" <td>12.755121</td>\n",
" <td>12.987085</td>\n",
" <td>13.328871</td>\n",
" <td>13.241964</td>\n",
" <td>2.947561</td>\n",
" <td>12.791541</td>\n",
" <td>...</td>\n",
" <td>12.878790</td>\n",
" <td>13.138233</td>\n",
" <td>12.970985</td>\n",
" <td>12.558581</td>\n",
" <td>13.419697</td>\n",
" <td>12.610037</td>\n",
" <td>12.449582</td>\n",
" <td>12.679300</td>\n",
" <td>12.432845</td>\n",
" <td>13.330623</td>\n",
" </tr>\n",
" <tr>\n",
" <th>FAM182B\\215487_x_at</th>\n",
" <td>1.759795</td>\n",
" <td>0.421856</td>\n",
" <td>4.997703</td>\n",
" <td>1.714052</td>\n",
" <td>3.881694</td>\n",
" <td>4.046220</td>\n",
" <td>2.018987</td>\n",
" <td>4.134714</td>\n",
" <td>2.393227</td>\n",
" <td>2.583846</td>\n",
" <td>...</td>\n",
" <td>2.849927</td>\n",
" <td>1.149526</td>\n",
" <td>3.348261</td>\n",
" <td>1.850631</td>\n",
" <td>0.647139</td>\n",
" <td>3.622649</td>\n",
" <td>4.407672</td>\n",
" <td>3.408984</td>\n",
" <td>3.727267</td>\n",
" <td>1.797312</td>\n",
" </tr>\n",
" <tr>\n",
" <th>C6orf108\\213871_s_at</th>\n",
" <td>3.582701</td>\n",
" <td>1.259200</td>\n",
" <td>2.048599</td>\n",
" <td>2.109661</td>\n",
" <td>3.604059</td>\n",
" <td>3.220994</td>\n",
" <td>1.206312</td>\n",
" <td>1.756195</td>\n",
" <td>0.354204</td>\n",
" <td>2.465766</td>\n",
" <td>...</td>\n",
" <td>2.053257</td>\n",
" <td>2.421000</td>\n",
" <td>3.287985</td>\n",
" <td>4.210568</td>\n",
" <td>2.441361</td>\n",
" <td>2.207599</td>\n",
" <td>2.172868</td>\n",
" <td>2.086094</td>\n",
" <td>1.788022</td>\n",
" <td>2.095864</td>\n",
" </tr>\n",
" <tr>\n",
" <th>CSRNP2\\225042_s_at</th>\n",
" <td>6.374174</td>\n",
" <td>4.883411</td>\n",
" <td>6.401555</td>\n",
" <td>6.514329</td>\n",
" <td>6.049038</td>\n",
" <td>5.922999</td>\n",
" <td>6.343104</td>\n",
" <td>7.006074</td>\n",
" <td>-1.647974</td>\n",
" <td>6.100008</td>\n",
" <td>...</td>\n",
" <td>5.625344</td>\n",
" <td>5.452931</td>\n",
" <td>6.387033</td>\n",
" <td>6.038015</td>\n",
" <td>6.148487</td>\n",
" <td>5.680344</td>\n",
" <td>5.882540</td>\n",
" <td>5.875183</td>\n",
" <td>6.261409</td>\n",
" <td>6.810057</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SLCO2B1\\203473_at</th>\n",
" <td>10.034813</td>\n",
" <td>8.756970</td>\n",
" <td>9.486851</td>\n",
" <td>9.691714</td>\n",
" <td>8.997532</td>\n",
" <td>9.316754</td>\n",
" <td>8.260534</td>\n",
" <td>9.819708</td>\n",
" <td>-1.396168</td>\n",
" <td>8.526370</td>\n",
" <td>...</td>\n",
" <td>8.346997</td>\n",
" <td>8.514296</td>\n",
" <td>9.381606</td>\n",
" <td>9.238491</td>\n",
" <td>9.320160</td>\n",
" <td>8.343523</td>\n",
" <td>8.400751</td>\n",
" <td>9.045113</td>\n",
" <td>8.889014</td>\n",
" <td>9.842943</td>\n",
" </tr>\n",
" <tr>\n",
" <th>MYNN\\237510_at</th>\n",
" <td>2.361996</td>\n",
" <td>0.114700</td>\n",
" <td>3.387004</td>\n",
" <td>2.883904</td>\n",
" <td>4.976735</td>\n",
" <td>3.417407</td>\n",
" <td>3.842748</td>\n",
" <td>4.088854</td>\n",
" <td>1.132814</td>\n",
" <td>3.943378</td>\n",
" <td>...</td>\n",
" <td>4.780258</td>\n",
" <td>3.285414</td>\n",
" <td>3.572114</td>\n",
" <td>4.307807</td>\n",
" <td>3.838034</td>\n",
" <td>3.913416</td>\n",
" <td>2.329247</td>\n",
" <td>3.460952</td>\n",
" <td>3.317411</td>\n",
" <td>4.770649</td>\n",
" </tr>\n",
" <tr>\n",
" <th>NAP1L1\\208752_x_at</th>\n",
" <td>10.628446</td>\n",
" <td>10.585366</td>\n",
" <td>10.177594</td>\n",
" <td>10.648825</td>\n",
" <td>10.851038</td>\n",
" <td>10.756323</td>\n",
" <td>10.402511</td>\n",
" <td>10.936770</td>\n",
" <td>-2.209909</td>\n",
" <td>10.745221</td>\n",
" <td>...</td>\n",
" <td>10.770474</td>\n",
" <td>9.792940</td>\n",
" <td>10.982587</td>\n",
" <td>10.398231</td>\n",
" <td>11.065046</td>\n",
" <td>10.883163</td>\n",
" <td>10.169750</td>\n",
" <td>10.456498</td>\n",
" <td>9.969458</td>\n",
" <td>11.191152</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ADAM28\\205997_at</th>\n",
" <td>5.450776</td>\n",
" <td>6.641620</td>\n",
" <td>4.300285</td>\n",
" <td>6.839683</td>\n",
" <td>5.465109</td>\n",
" <td>5.555887</td>\n",
" <td>3.875996</td>\n",
" <td>6.319249</td>\n",
" <td>-1.366403</td>\n",
" <td>4.995385</td>\n",
" <td>...</td>\n",
" <td>3.859880</td>\n",
" <td>5.675847</td>\n",
" <td>2.037948</td>\n",
" <td>5.234149</td>\n",
" <td>6.298711</td>\n",
" <td>5.129015</td>\n",
" <td>4.205901</td>\n",
" <td>5.297874</td>\n",
" <td>3.993122</td>\n",
" <td>5.034577</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100507248\\235236_at</th>\n",
" <td>0.841828</td>\n",
" <td>3.184030</td>\n",
" <td>1.062971</td>\n",
" <td>1.479386</td>\n",
" <td>1.279673</td>\n",
" <td>-1.013605</td>\n",
" <td>2.399652</td>\n",
" <td>-1.327830</td>\n",
" <td>0.643810</td>\n",
" <td>2.481676</td>\n",
" <td>...</td>\n",
" <td>0.497914</td>\n",
" <td>2.766845</td>\n",
" <td>1.421420</td>\n",
" <td>0.274554</td>\n",
" <td>2.516663</td>\n",
" <td>3.578105</td>\n",
" <td>2.022162</td>\n",
" <td>2.553985</td>\n",
" <td>-0.141042</td>\n",
" <td>3.280830</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PHF8\\238837_at</th>\n",
" <td>0.414558</td>\n",
" <td>0.418255</td>\n",
" <td>0.683068</td>\n",
" <td>-0.057428</td>\n",
" <td>0.478299</td>\n",
" <td>0.191297</td>\n",
" <td>0.053806</td>\n",
" <td>2.333670</td>\n",
" <td>-1.051005</td>\n",
" <td>0.881030</td>\n",
" <td>...</td>\n",
" <td>1.816514</td>\n",
" <td>0.384713</td>\n",
" <td>2.759429</td>\n",
" <td>0.919752</td>\n",
" <td>0.762944</td>\n",
" <td>1.900142</td>\n",
" <td>-0.200908</td>\n",
" <td>0.260471</td>\n",
" <td>0.137333</td>\n",
" <td>1.619676</td>\n",
" </tr>\n",
" <tr>\n",
" <th>C9orf96\\1554787_at</th>\n",
" <td>4.105762</td>\n",
" <td>1.087877</td>\n",
" <td>1.965241</td>\n",
" <td>0.014298</td>\n",
" <td>4.360371</td>\n",
" <td>4.244400</td>\n",
" <td>2.258263</td>\n",
" <td>1.780310</td>\n",
" <td>2.060843</td>\n",
" <td>3.286591</td>\n",
" <td>...</td>\n",
" <td>1.401762</td>\n",
" <td>3.062583</td>\n",
" <td>4.032815</td>\n",
" <td>2.085414</td>\n",
" <td>3.011116</td>\n",
" <td>1.542263</td>\n",
" <td>2.884143</td>\n",
" <td>3.452595</td>\n",
" <td>3.633559</td>\n",
" <td>0.805144</td>\n",
" </tr>\n",
" <tr>\n",
" <th>TNPO2\\210585_s_at</th>\n",
" <td>4.113917</td>\n",
" <td>0.407559</td>\n",
" <td>2.646727</td>\n",
" <td>4.812313</td>\n",
" <td>3.139695</td>\n",
" <td>4.940749</td>\n",
" <td>3.838054</td>\n",
" <td>5.018616</td>\n",
" <td>-0.675588</td>\n",
" <td>2.092505</td>\n",
" <td>...</td>\n",
" <td>1.812305</td>\n",
" <td>1.708638</td>\n",
" <td>2.571538</td>\n",
" <td>4.306955</td>\n",
" <td>3.045516</td>\n",
" <td>1.792347</td>\n",
" <td>2.022006</td>\n",
" <td>2.772952</td>\n",
" <td>3.268816</td>\n",
" <td>3.725119</td>\n",
" </tr>\n",
" <tr>\n",
" <th>FLJ31485\\239569_at</th>\n",
" <td>3.371838</td>\n",
" <td>2.244808</td>\n",
" <td>4.399171</td>\n",
" <td>3.569661</td>\n",
" <td>2.099006</td>\n",
" <td>5.009110</td>\n",
" <td>3.630510</td>\n",
" <td>4.570056</td>\n",
" <td>-0.911096</td>\n",
" <td>4.624698</td>\n",
" <td>...</td>\n",
" <td>4.128005</td>\n",
" <td>2.735113</td>\n",
" <td>5.520036</td>\n",
" <td>4.637552</td>\n",
" <td>4.818927</td>\n",
" <td>3.922987</td>\n",
" <td>4.594638</td>\n",
" <td>4.220338</td>\n",
" <td>4.644427</td>\n",
" <td>4.110689</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PUM1\\201164_s_at</th>\n",
" <td>9.192882</td>\n",
" <td>8.685846</td>\n",
" <td>8.694556</td>\n",
" <td>8.958501</td>\n",
" <td>9.190432</td>\n",
" <td>8.840312</td>\n",
" <td>8.274676</td>\n",
" <td>9.174604</td>\n",
" <td>1.454344</td>\n",
" <td>8.494348</td>\n",
" <td>...</td>\n",
" <td>9.462829</td>\n",
" <td>8.449215</td>\n",
" <td>9.270368</td>\n",
" <td>8.673532</td>\n",
" <td>9.521914</td>\n",
" <td>9.425923</td>\n",
" <td>8.175694</td>\n",
" <td>8.123552</td>\n",
" <td>8.278528</td>\n",
" <td>9.520827</td>\n",
" </tr>\n",
" <tr>\n",
" <th>COX4I1\\202698_x_at</th>\n",
" <td>11.424980</td>\n",
" <td>11.025444</td>\n",
" <td>10.975160</td>\n",
" <td>11.094902</td>\n",
" <td>10.266833</td>\n",
" <td>11.072702</td>\n",
" <td>10.950461</td>\n",
" <td>11.406848</td>\n",
" <td>-1.125409</td>\n",
" <td>10.633368</td>\n",
" <td>...</td>\n",
" <td>10.422706</td>\n",
" <td>10.628227</td>\n",
" <td>10.927074</td>\n",
" <td>10.536451</td>\n",
" <td>11.284066</td>\n",
" <td>10.729723</td>\n",
" <td>10.442591</td>\n",
" <td>10.516931</td>\n",
" <td>10.675004</td>\n",
" <td>11.483045</td>\n",
" </tr>\n",
" <tr>\n",
" <th>IZUMO4\\215734_at</th>\n",
" <td>5.042977</td>\n",
" <td>2.857635</td>\n",
" <td>4.268292</td>\n",
" <td>4.661282</td>\n",
" <td>4.639140</td>\n",
" <td>4.592122</td>\n",
" <td>4.583639</td>\n",
" <td>4.245769</td>\n",
" <td>-2.438604</td>\n",
" <td>2.911114</td>\n",
" <td>...</td>\n",
" <td>3.221716</td>\n",
" <td>3.966920</td>\n",
" <td>2.208118</td>\n",
" <td>4.387459</td>\n",
" <td>3.835853</td>\n",
" <td>3.551934</td>\n",
" <td>3.564061</td>\n",
" <td>5.134899</td>\n",
" <td>3.869950</td>\n",
" <td>4.971139</td>\n",
" </tr>\n",
" <tr>\n",
" <th>TPSAB1\\216485_s_at</th>\n",
" <td>0.137189</td>\n",
" <td>2.176741</td>\n",
" <td>1.948201</td>\n",
" <td>4.195206</td>\n",
" <td>2.251562</td>\n",
" <td>0.251071</td>\n",
" <td>2.022698</td>\n",
" <td>2.780024</td>\n",
" <td>0.424202</td>\n",
" <td>0.800877</td>\n",
" <td>...</td>\n",
" <td>0.322597</td>\n",
" <td>0.241108</td>\n",
" <td>1.373153</td>\n",
" <td>0.022361</td>\n",
" <td>0.703632</td>\n",
" <td>1.926417</td>\n",
" <td>0.645914</td>\n",
" <td>1.024490</td>\n",
" <td>-0.121292</td>\n",
" <td>1.646753</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LMAN1L\\220420_at</th>\n",
" <td>1.562934</td>\n",
" <td>3.100598</td>\n",
" <td>1.747254</td>\n",
" <td>3.675906</td>\n",
" <td>3.429080</td>\n",
" <td>1.925282</td>\n",
" <td>1.608904</td>\n",
" <td>1.616240</td>\n",
" <td>2.044873</td>\n",
" <td>1.861777</td>\n",
" <td>...</td>\n",
" <td>3.166168</td>\n",
" <td>0.785910</td>\n",
" <td>4.803460</td>\n",
" <td>1.394646</td>\n",
" <td>2.410542</td>\n",
" <td>2.427598</td>\n",
" <td>2.189227</td>\n",
" <td>2.269497</td>\n",
" <td>1.488505</td>\n",
" <td>2.667940</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LY6K\\223687_s_at</th>\n",
" <td>1.228997</td>\n",
" <td>3.534535</td>\n",
" <td>3.803702</td>\n",
" <td>4.598181</td>\n",
" <td>3.881948</td>\n",
" <td>1.130984</td>\n",
" <td>4.844717</td>\n",
" <td>4.438838</td>\n",
" <td>0.294900</td>\n",
" <td>3.856249</td>\n",
" <td>...</td>\n",
" <td>4.182668</td>\n",
" <td>1.804074</td>\n",
" <td>4.364804</td>\n",
" <td>2.702303</td>\n",
" <td>1.110316</td>\n",
" <td>4.526626</td>\n",
" <td>4.010046</td>\n",
" <td>2.707023</td>\n",
" <td>3.570839</td>\n",
" <td>3.322880</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ACAD10\\238655_at</th>\n",
" <td>4.785132</td>\n",
" <td>1.079429</td>\n",
" <td>4.897531</td>\n",
" <td>1.068464</td>\n",
" <td>3.974392</td>\n",
" <td>5.051342</td>\n",
" <td>4.244278</td>\n",
" <td>4.565335</td>\n",
" <td>-0.332001</td>\n",
" <td>4.354438</td>\n",
" <td>...</td>\n",
" <td>4.449951</td>\n",
" <td>3.581809</td>\n",
" <td>5.354794</td>\n",
" <td>4.535288</td>\n",
" <td>4.514318</td>\n",
" <td>5.121140</td>\n",
" <td>3.469222</td>\n",
" <td>3.874984</td>\n",
" <td>4.280593</td>\n",
" <td>4.871326</td>\n",
" </tr>\n",
" <tr>\n",
" <th>TIMM22\\219184_x_at</th>\n",
" <td>6.169121</td>\n",
" <td>5.517953</td>\n",
" <td>6.243324</td>\n",
" <td>6.358511</td>\n",
" <td>6.519636</td>\n",
" <td>5.950811</td>\n",
" <td>4.830484</td>\n",
" <td>6.513282</td>\n",
" <td>0.089715</td>\n",
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" <td>5.784881</td>\n",
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" <td>6.477974</td>\n",
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" <td>4.779969</td>\n",
" <td>5.288362</td>\n",
" <td>5.545894</td>\n",
" <td>6.244668</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HUS1\\217618_x_at</th>\n",
" <td>5.018104</td>\n",
" <td>4.675059</td>\n",
" <td>6.151751</td>\n",
" <td>5.439500</td>\n",
" <td>5.783855</td>\n",
" <td>6.387462</td>\n",
" <td>4.663669</td>\n",
" <td>5.843750</td>\n",
" <td>1.564685</td>\n",
" <td>6.010276</td>\n",
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" <td>5.769928</td>\n",
" <td>5.373325</td>\n",
" <td>5.535664</td>\n",
" <td>5.604062</td>\n",
" <td>5.633858</td>\n",
" <td>6.031278</td>\n",
" <td>5.453458</td>\n",
" <td>5.839237</td>\n",
" <td>5.774929</td>\n",
" <td>5.465534</td>\n",
" </tr>\n",
" <tr>\n",
" <th>EPHA7\\206852_at</th>\n",
" <td>3.069138</td>\n",
" <td>3.238351</td>\n",
" <td>3.662547</td>\n",
" <td>-0.638656</td>\n",
" <td>3.145749</td>\n",
" <td>2.637562</td>\n",
" <td>3.774987</td>\n",
" <td>0.199914</td>\n",
" <td>-1.506381</td>\n",
" <td>3.202302</td>\n",
" <td>...</td>\n",
" <td>3.590913</td>\n",
" <td>1.877579</td>\n",
" <td>1.158111</td>\n",
" <td>0.885106</td>\n",
" <td>2.495519</td>\n",
" <td>0.404598</td>\n",
" <td>3.397789</td>\n",
" <td>-0.173467</td>\n",
" <td>2.728247</td>\n",
" <td>3.904648</td>\n",
" </tr>\n",
" <tr>\n",
" <th>CSH1\\208069_x_at</th>\n",
" <td>1.359319</td>\n",
" <td>0.969477</td>\n",
" <td>1.082062</td>\n",
" <td>0.112980</td>\n",
" <td>1.229982</td>\n",
" <td>1.225509</td>\n",
" <td>0.164168</td>\n",
" <td>0.208342</td>\n",
" <td>-0.527080</td>\n",
" <td>-0.023990</td>\n",
" <td>...</td>\n",
" <td>0.494426</td>\n",
" <td>0.546393</td>\n",
" <td>1.646955</td>\n",
" <td>0.601506</td>\n",
" <td>3.274652</td>\n",
" <td>0.575980</td>\n",
" <td>2.113977</td>\n",
" <td>0.268351</td>\n",
" <td>0.506419</td>\n",
" <td>1.501908</td>\n",
" </tr>\n",
" <tr>\n",
" <th>FMNL2\\242665_at</th>\n",
" <td>5.583281</td>\n",
" <td>4.859274</td>\n",
" <td>6.557625</td>\n",
" <td>5.519202</td>\n",
" <td>6.182331</td>\n",
" <td>5.753663</td>\n",
" <td>3.526682</td>\n",
" <td>5.483925</td>\n",
" <td>-1.352127</td>\n",
" <td>6.537523</td>\n",
" <td>...</td>\n",
" <td>6.091905</td>\n",
" <td>4.495970</td>\n",
" <td>5.993219</td>\n",
" <td>6.431006</td>\n",
" <td>4.795767</td>\n",
" <td>6.155328</td>\n",
" <td>7.011809</td>\n",
" <td>5.865367</td>\n",
" <td>6.039472</td>\n",
" <td>5.152058</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PUS3\\221277_s_at</th>\n",
" <td>6.631467</td>\n",
" <td>6.873272</td>\n",
" <td>6.322101</td>\n",
" <td>7.021946</td>\n",
" <td>6.664013</td>\n",
" <td>6.887208</td>\n",
" <td>5.809250</td>\n",
" <td>7.054393</td>\n",
" <td>-1.097996</td>\n",
" <td>6.323484</td>\n",
" <td>...</td>\n",
" <td>6.953766</td>\n",
" <td>5.959842</td>\n",
" <td>6.140368</td>\n",
" <td>6.310242</td>\n",
" <td>6.235164</td>\n",
" <td>6.703793</td>\n",
" <td>6.611894</td>\n",
" <td>6.316678</td>\n",
" <td>5.945692</td>\n",
" <td>7.125858</td>\n",
" </tr>\n",
" <tr>\n",
" <th>CELF4\\231220_at</th>\n",
" <td>0.441579</td>\n",
" <td>-0.481415</td>\n",
" <td>2.454702</td>\n",
" <td>2.611196</td>\n",
" <td>0.427831</td>\n",
" <td>2.381018</td>\n",
" <td>-0.357444</td>\n",
" <td>3.528621</td>\n",
" <td>0.402307</td>\n",
" <td>-0.135939</td>\n",
" <td>...</td>\n",
" <td>0.166548</td>\n",
" <td>-0.291474</td>\n",
" <td>0.519119</td>\n",
" <td>2.435509</td>\n",
" <td>0.474109</td>\n",
" <td>3.179498</td>\n",
" <td>2.003573</td>\n",
" <td>0.316586</td>\n",
" <td>-0.800551</td>\n",
" <td>-0.160679</td>\n",
" </tr>\n",
" <tr>\n",
" <th>RBM6\\228030_at</th>\n",
" <td>9.486984</td>\n",
" <td>9.160928</td>\n",
" <td>10.017463</td>\n",
" <td>9.410869</td>\n",
" <td>9.978954</td>\n",
" <td>8.680039</td>\n",
" <td>8.188223</td>\n",
" <td>9.498291</td>\n",
" <td>2.064152</td>\n",
" <td>9.045170</td>\n",
" <td>...</td>\n",
" <td>9.580609</td>\n",
" <td>9.308680</td>\n",
" <td>9.745452</td>\n",
" <td>8.250696</td>\n",
" <td>9.392914</td>\n",
" <td>10.222855</td>\n",
" <td>7.912560</td>\n",
" <td>7.941529</td>\n",
" <td>8.808716</td>\n",
" <td>9.672188</td>\n",
" </tr>\n",
" <tr>\n",
" <th>AVIL\\233333_x_at</th>\n",
" <td>5.856667</td>\n",
" <td>5.921548</td>\n",
" <td>7.078343</td>\n",
" <td>6.954941</td>\n",
" <td>7.159518</td>\n",
" <td>6.541760</td>\n",
" <td>6.083077</td>\n",
" <td>7.272760</td>\n",
" <td>3.514526</td>\n",
" <td>6.478228</td>\n",
" <td>...</td>\n",
" <td>7.190635</td>\n",
" <td>5.107085</td>\n",
" <td>7.709208</td>\n",
" <td>6.657111</td>\n",
" <td>6.573403</td>\n",
" <td>6.356035</td>\n",
" <td>6.471448</td>\n",
" <td>6.134972</td>\n",
" <td>6.028686</td>\n",
" <td>7.222264</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>MON1B\\233557_s_at</th>\n",
" <td>7.322334</td>\n",
" <td>5.598157</td>\n",
" <td>7.301825</td>\n",
" <td>7.463622</td>\n",
" <td>6.327718</td>\n",
" <td>6.466811</td>\n",
" <td>7.060609</td>\n",
" <td>8.283028</td>\n",
" <td>1.551398</td>\n",
" <td>6.111117</td>\n",
" <td>...</td>\n",
" <td>6.411186</td>\n",
" <td>6.440970</td>\n",
" <td>7.718211</td>\n",
" <td>6.492505</td>\n",
" <td>7.361803</td>\n",
" <td>6.280071</td>\n",
" <td>6.643899</td>\n",
" <td>7.154373</td>\n",
" <td>6.405061</td>\n",
" <td>6.969646</td>\n",
" </tr>\n",
" <tr>\n",
" <th>CLLU1\\1558185_at</th>\n",
" <td>3.180862</td>\n",
" <td>3.434628</td>\n",
" <td>1.344834</td>\n",
" <td>3.800320</td>\n",
" <td>2.806260</td>\n",
" <td>-0.134157</td>\n",
" <td>2.790488</td>\n",
" <td>3.794156</td>\n",
" <td>1.574295</td>\n",
" <td>3.283889</td>\n",
" <td>...</td>\n",
" <td>-0.200051</td>\n",
" <td>3.760445</td>\n",
" <td>1.356854</td>\n",
" <td>-0.964424</td>\n",
" <td>0.124328</td>\n",
" <td>0.007009</td>\n",
" <td>3.227231</td>\n",
" <td>0.525067</td>\n",
" <td>2.545576</td>\n",
" <td>0.386038</td>\n",
" </tr>\n",
" <tr>\n",
" <th>KTN1\\214709_s_at</th>\n",
" <td>9.996389</td>\n",
" <td>9.792563</td>\n",
" <td>10.114302</td>\n",
" <td>9.761053</td>\n",
" <td>10.761277</td>\n",
" <td>10.352209</td>\n",
" <td>9.292545</td>\n",
" <td>10.518791</td>\n",
" <td>1.246262</td>\n",
" <td>10.112453</td>\n",
" <td>...</td>\n",
" <td>10.828573</td>\n",
" <td>9.403285</td>\n",
" <td>10.343597</td>\n",
" <td>9.697475</td>\n",
" <td>10.437482</td>\n",
" <td>10.219253</td>\n",
" <td>9.777232</td>\n",
" <td>9.765666</td>\n",
" <td>9.429413</td>\n",
" <td>10.550237</td>\n",
" </tr>\n",
" <tr>\n",
" <th>KRTAP4-7\\216810_at</th>\n",
" <td>2.492058</td>\n",
" <td>1.778827</td>\n",
" <td>2.818088</td>\n",
" <td>0.879745</td>\n",
" <td>2.604634</td>\n",
" <td>2.112997</td>\n",
" <td>4.064762</td>\n",
" <td>2.740112</td>\n",
" <td>1.139371</td>\n",
" <td>2.688896</td>\n",
" <td>...</td>\n",
" <td>3.299444</td>\n",
" <td>2.225593</td>\n",
" <td>4.368468</td>\n",
" <td>1.189622</td>\n",
" <td>4.000316</td>\n",
" <td>2.156096</td>\n",
" <td>2.231165</td>\n",
" <td>3.906371</td>\n",
" <td>2.807456</td>\n",
" <td>1.700799</td>\n",
" </tr>\n",
" <tr>\n",
" <th>RBKS\\219222_at</th>\n",
" <td>6.212774</td>\n",
" <td>5.976840</td>\n",
" <td>5.731031</td>\n",
" <td>6.378312</td>\n",
" <td>5.044739</td>\n",
" <td>4.772419</td>\n",
" <td>5.608419</td>\n",
" <td>6.695047</td>\n",
" <td>1.178052</td>\n",
" <td>4.758532</td>\n",
" <td>...</td>\n",
" <td>5.539295</td>\n",
" <td>5.411389</td>\n",
" <td>6.204941</td>\n",
" <td>4.763821</td>\n",
" <td>5.966758</td>\n",
" <td>5.916391</td>\n",
" <td>4.946553</td>\n",
" <td>5.777888</td>\n",
" <td>4.430118</td>\n",
" <td>6.200583</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100506621\\227061_at</th>\n",
" <td>7.323550</td>\n",
" <td>7.469943</td>\n",
" <td>9.200810</td>\n",
" <td>7.576832</td>\n",
" <td>7.448273</td>\n",
" <td>6.004852</td>\n",
" <td>7.770505</td>\n",
" <td>8.117565</td>\n",
" <td>1.858896</td>\n",
" <td>8.021902</td>\n",
" <td>...</td>\n",
" <td>6.946345</td>\n",
" <td>7.382287</td>\n",
" <td>8.425191</td>\n",
" <td>6.190012</td>\n",
" <td>7.384905</td>\n",
" <td>7.763080</td>\n",
" <td>7.322523</td>\n",
" <td>6.880881</td>\n",
" <td>7.502840</td>\n",
" <td>8.017187</td>\n",
" </tr>\n",
" <tr>\n",
" <th>CCDC67\\1554071_at</th>\n",
" <td>1.965267</td>\n",
" <td>2.750519</td>\n",
" <td>0.020598</td>\n",
" <td>3.295987</td>\n",
" <td>0.489317</td>\n",
" <td>-0.952302</td>\n",
" <td>2.846279</td>\n",
" <td>1.156487</td>\n",
" <td>-4.174082</td>\n",
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" <td>...</td>\n",
" <td>0.700120</td>\n",
" <td>-0.228895</td>\n",
" <td>2.423452</td>\n",
" <td>0.243413</td>\n",
" <td>3.231492</td>\n",
" <td>0.267464</td>\n",
" <td>2.338519</td>\n",
" <td>2.860540</td>\n",
" <td>0.016924</td>\n",
" <td>-0.710642</td>\n",
" </tr>\n",
" <tr>\n",
" <th>MCM9\\219673_at</th>\n",
" <td>6.303923</td>\n",
" <td>5.747465</td>\n",
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" <td>6.292412</td>\n",
" <td>6.461627</td>\n",
" <td>6.652888</td>\n",
" <td>5.325278</td>\n",
" <td>6.556319</td>\n",
" <td>1.405235</td>\n",
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" <td>...</td>\n",
" <td>6.156712</td>\n",
" <td>5.207772</td>\n",
" <td>6.062892</td>\n",
" <td>6.130558</td>\n",
" <td>6.280587</td>\n",
" <td>5.896870</td>\n",
" <td>6.141386</td>\n",
" <td>5.830752</td>\n",
" <td>6.055306</td>\n",
" <td>6.385132</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC730101\\213248_at</th>\n",
" <td>5.458103</td>\n",
" <td>6.042692</td>\n",
" <td>5.830443</td>\n",
" <td>5.714144</td>\n",
" <td>6.086276</td>\n",
" <td>5.952103</td>\n",
" <td>4.264191</td>\n",
" <td>5.974096</td>\n",
" <td>-0.235853</td>\n",
" <td>5.628036</td>\n",
" <td>...</td>\n",
" <td>6.084107</td>\n",
" <td>5.177093</td>\n",
" <td>5.802333</td>\n",
" <td>5.042351</td>\n",
" <td>5.277966</td>\n",
" <td>6.093664</td>\n",
" <td>5.559908</td>\n",
" <td>4.932529</td>\n",
" <td>4.992519</td>\n",
" <td>6.580990</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100508546\\244037_at</th>\n",
" <td>4.314747</td>\n",
" <td>4.632012</td>\n",
" <td>4.600192</td>\n",
" <td>4.657777</td>\n",
" <td>6.033800</td>\n",
" <td>3.933337</td>\n",
" <td>1.383160</td>\n",
" <td>4.898866</td>\n",
" <td>-1.920762</td>\n",
" <td>4.565877</td>\n",
" <td>...</td>\n",
" <td>3.729879</td>\n",
" <td>3.069190</td>\n",
" <td>2.968163</td>\n",
" <td>4.364895</td>\n",
" <td>1.032228</td>\n",
" <td>3.603454</td>\n",
" <td>2.715448</td>\n",
" <td>1.065910</td>\n",
" <td>3.543595</td>\n",
" <td>4.800848</td>\n",
" </tr>\n",
" <tr>\n",
" <th>RNPS1\\200060_s_at</th>\n",
" <td>9.180869</td>\n",
" <td>9.034972</td>\n",
" <td>9.006116</td>\n",
" <td>9.652415</td>\n",
" <td>8.701539</td>\n",
" <td>9.218159</td>\n",
" <td>8.672252</td>\n",
" <td>10.146887</td>\n",
" <td>0.158815</td>\n",
" <td>8.911913</td>\n",
" <td>...</td>\n",
" <td>8.891999</td>\n",
" <td>7.953981</td>\n",
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" <td>9.062535</td>\n",
" <td>9.309429</td>\n",
" <td>8.807416</td>\n",
" <td>8.851462</td>\n",
" <td>8.927802</td>\n",
" <td>8.675572</td>\n",
" <td>9.464456</td>\n",
" </tr>\n",
" <tr>\n",
" <th>C8orf74\\1569246_a_at</th>\n",
" <td>3.316081</td>\n",
" <td>1.549364</td>\n",
" <td>2.521832</td>\n",
" <td>4.597054</td>\n",
" <td>5.367626</td>\n",
" <td>4.720995</td>\n",
" <td>3.966809</td>\n",
" <td>4.746420</td>\n",
" <td>1.012318</td>\n",
" <td>1.834861</td>\n",
" <td>...</td>\n",
" <td>4.522859</td>\n",
" <td>4.420981</td>\n",
" <td>5.963370</td>\n",
" <td>4.814381</td>\n",
" <td>3.303941</td>\n",
" <td>4.218324</td>\n",
" <td>4.396194</td>\n",
" <td>1.711301</td>\n",
" <td>4.925235</td>\n",
" <td>1.969815</td>\n",
" </tr>\n",
" <tr>\n",
" <th>UTP14C\\203614_at</th>\n",
" <td>8.437311</td>\n",
" <td>7.923203</td>\n",
" <td>7.907924</td>\n",
" <td>8.131415</td>\n",
" <td>8.309217</td>\n",
" <td>8.235052</td>\n",
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" <td>8.601734</td>\n",
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" <td>...</td>\n",
" <td>8.575717</td>\n",
" <td>7.755288</td>\n",
" <td>8.397606</td>\n",
" <td>8.035178</td>\n",
" <td>8.590939</td>\n",
" <td>8.551051</td>\n",
" <td>7.873912</td>\n",
" <td>7.310994</td>\n",
" <td>7.716230</td>\n",
" <td>8.639301</td>\n",
" </tr>\n",
" <tr>\n",
" <th>RHEB\\201452_at</th>\n",
" <td>4.676200</td>\n",
" <td>1.578282</td>\n",
" <td>4.372318</td>\n",
" <td>3.111474</td>\n",
" <td>0.485128</td>\n",
" <td>2.154006</td>\n",
" <td>4.723782</td>\n",
" <td>4.633396</td>\n",
" <td>-0.604369</td>\n",
" <td>2.497939</td>\n",
" <td>...</td>\n",
" <td>0.429171</td>\n",
" <td>3.956540</td>\n",
" <td>1.644807</td>\n",
" <td>4.890461</td>\n",
" <td>4.466386</td>\n",
" <td>4.500146</td>\n",
" <td>2.375757</td>\n",
" <td>4.207651</td>\n",
" <td>3.423995</td>\n",
" <td>4.421594</td>\n",
" </tr>\n",
" <tr>\n",
" <th>CXCL16\\223454_at</th>\n",
" <td>9.465360</td>\n",
" <td>8.289337</td>\n",
" <td>9.233644</td>\n",
" <td>9.871523</td>\n",
" <td>8.590482</td>\n",
" <td>9.214773</td>\n",
" <td>8.601964</td>\n",
" <td>9.486413</td>\n",
" <td>0.336123</td>\n",
" <td>8.215048</td>\n",
" <td>...</td>\n",
" <td>7.689760</td>\n",
" <td>8.066676</td>\n",
" <td>8.979814</td>\n",
" <td>8.720945</td>\n",
" <td>8.943913</td>\n",
" <td>8.278789</td>\n",
" <td>8.592207</td>\n",
" <td>8.964350</td>\n",
" <td>8.768965</td>\n",
" <td>9.031031</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PSPC1\\218371_s_at</th>\n",
" <td>7.101902</td>\n",
" <td>6.961612</td>\n",
" <td>7.179372</td>\n",
" <td>7.431514</td>\n",
" <td>7.177051</td>\n",
" <td>7.279490</td>\n",
" <td>6.230136</td>\n",
" <td>7.889607</td>\n",
" <td>-2.234112</td>\n",
" <td>7.393090</td>\n",
" <td>...</td>\n",
" <td>7.131188</td>\n",
" <td>5.947082</td>\n",
" <td>7.035789</td>\n",
" <td>7.294244</td>\n",
" <td>7.477669</td>\n",
" <td>6.826167</td>\n",
" <td>6.530594</td>\n",
" <td>6.498798</td>\n",
" <td>6.342836</td>\n",
" <td>7.471773</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SIK3\\213034_at</th>\n",
" <td>7.888189</td>\n",
" <td>7.736754</td>\n",
" <td>7.553514</td>\n",
" <td>7.753431</td>\n",
" <td>7.962983</td>\n",
" <td>7.863926</td>\n",
" <td>7.978013</td>\n",
" <td>8.554777</td>\n",
" <td>1.962497</td>\n",
" <td>7.728315</td>\n",
" <td>...</td>\n",
" <td>8.131667</td>\n",
" <td>7.260054</td>\n",
" <td>7.847640</td>\n",
" <td>7.622147</td>\n",
" <td>8.259889</td>\n",
" <td>7.620117</td>\n",
" <td>7.406698</td>\n",
" <td>7.638400</td>\n",
" <td>7.422620</td>\n",
" <td>8.434107</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ACOT9\\221641_s_at</th>\n",
" <td>9.054124</td>\n",
" <td>8.092091</td>\n",
" <td>8.246622</td>\n",
" <td>8.634089</td>\n",
" <td>7.678487</td>\n",
" <td>8.523825</td>\n",
" <td>9.248853</td>\n",
" <td>9.179200</td>\n",
" <td>-0.759507</td>\n",
" <td>7.814621</td>\n",
" <td>...</td>\n",
" <td>7.840388</td>\n",
" <td>7.504215</td>\n",
" <td>8.411443</td>\n",
" <td>7.790433</td>\n",
" <td>8.638139</td>\n",
" <td>8.072674</td>\n",
" <td>7.603500</td>\n",
" <td>8.391544</td>\n",
" <td>8.262889</td>\n",
" <td>8.341719</td>\n",
" </tr>\n",
" <tr>\n",
" <th>KIAA1661\\215943_at</th>\n",
" <td>3.452543</td>\n",
" <td>2.797194</td>\n",
" <td>3.073855</td>\n",
" <td>0.238921</td>\n",
" <td>0.288016</td>\n",
" <td>2.898096</td>\n",
" <td>3.284806</td>\n",
" <td>4.135313</td>\n",
" <td>1.865974</td>\n",
" <td>1.637773</td>\n",
" <td>...</td>\n",
" <td>1.571546</td>\n",
" <td>0.154868</td>\n",
" <td>4.131713</td>\n",
" <td>0.860454</td>\n",
" <td>0.499435</td>\n",
" <td>4.370729</td>\n",
" <td>2.558929</td>\n",
" <td>-0.026417</td>\n",
" <td>0.001269</td>\n",
" <td>3.834772</td>\n",
" </tr>\n",
" <tr>\n",
" <th>STEAP2\\225871_at</th>\n",
" <td>6.958019</td>\n",
" <td>8.671654</td>\n",
" <td>7.542428</td>\n",
" <td>7.343310</td>\n",
" <td>6.991034</td>\n",
" <td>6.901712</td>\n",
" <td>8.131980</td>\n",
" <td>7.544254</td>\n",
" <td>-1.019691</td>\n",
" <td>6.642846</td>\n",
" <td>...</td>\n",
" <td>7.170436</td>\n",
" <td>5.926773</td>\n",
" <td>6.827387</td>\n",
" <td>6.316084</td>\n",
" <td>6.746796</td>\n",
" <td>7.101986</td>\n",
" <td>6.221703</td>\n",
" <td>7.338317</td>\n",
" <td>5.990190</td>\n",
" <td>7.061323</td>\n",
" </tr>\n",
" <tr>\n",
" <th>AKAP5\\207800_at</th>\n",
" <td>1.097725</td>\n",
" <td>1.830588</td>\n",
" <td>1.652087</td>\n",
" <td>1.086485</td>\n",
" <td>0.702108</td>\n",
" <td>1.539263</td>\n",
" <td>0.980252</td>\n",
" <td>0.912205</td>\n",
" <td>-2.130511</td>\n",
" <td>3.373133</td>\n",
" <td>...</td>\n",
" <td>3.239957</td>\n",
" <td>1.053104</td>\n",
" <td>3.483132</td>\n",
" <td>3.388520</td>\n",
" <td>1.650944</td>\n",
" <td>0.955037</td>\n",
" <td>0.808261</td>\n",
" <td>2.180963</td>\n",
" <td>1.017908</td>\n",
" <td>3.116330</td>\n",
" </tr>\n",
" <tr>\n",
" <th>C1orf57\\223272_s_at</th>\n",
" <td>6.872743</td>\n",
" <td>5.970815</td>\n",
" <td>6.643149</td>\n",
" <td>6.758743</td>\n",
" <td>6.745412</td>\n",
" <td>6.706544</td>\n",
" <td>6.514338</td>\n",
" <td>7.202809</td>\n",
" <td>-1.962480</td>\n",
" <td>6.704014</td>\n",
" <td>...</td>\n",
" <td>6.740887</td>\n",
" <td>6.595195</td>\n",
" <td>6.685015</td>\n",
" <td>7.120300</td>\n",
" <td>7.355307</td>\n",
" <td>6.374612</td>\n",
" <td>6.479274</td>\n",
" <td>4.271597</td>\n",
" <td>6.080555</td>\n",
" <td>7.493967</td>\n",
" </tr>\n",
" <tr>\n",
" <th>C7orf30\\226385_s_at</th>\n",
" <td>9.253008</td>\n",
" <td>9.173635</td>\n",
" <td>8.618015</td>\n",
" <td>9.345833</td>\n",
" <td>8.935483</td>\n",
" <td>9.336312</td>\n",
" <td>8.811998</td>\n",
" <td>9.851763</td>\n",
" <td>1.506125</td>\n",
" <td>9.122683</td>\n",
" <td>...</td>\n",
" <td>9.229444</td>\n",
" <td>8.423028</td>\n",
" <td>9.110016</td>\n",
" <td>9.052321</td>\n",
" <td>9.141443</td>\n",
" <td>9.071116</td>\n",
" <td>8.933115</td>\n",
" <td>8.766519</td>\n",
" <td>8.582187</td>\n",
" <td>9.743210</td>\n",
" </tr>\n",
" <tr>\n",
" <th>BAX\\208478_s_at</th>\n",
" <td>5.946710</td>\n",
" <td>5.331426</td>\n",
" <td>5.553677</td>\n",
" <td>5.729118</td>\n",
" <td>3.767771</td>\n",
" <td>6.915808</td>\n",
" <td>4.501866</td>\n",
" <td>5.761283</td>\n",
" <td>2.141668</td>\n",
" <td>6.202324</td>\n",
" <td>...</td>\n",
" <td>4.750446</td>\n",
" <td>4.550014</td>\n",
" <td>5.028887</td>\n",
" <td>6.286889</td>\n",
" <td>5.575055</td>\n",
" <td>5.071591</td>\n",
" <td>5.964729</td>\n",
" <td>6.437599</td>\n",
" <td>5.580124</td>\n",
" <td>5.227425</td>\n",
" </tr>\n",
" <tr>\n",
" <th>MAN1C1\\218918_at</th>\n",
" <td>6.990875</td>\n",
" <td>6.941024</td>\n",
" <td>6.985261</td>\n",
" <td>6.772004</td>\n",
" <td>6.583388</td>\n",
" <td>6.742747</td>\n",
" <td>6.217508</td>\n",
" <td>7.655159</td>\n",
" <td>1.364606</td>\n",
" <td>6.778117</td>\n",
" <td>...</td>\n",
" <td>6.401467</td>\n",
" <td>6.305770</td>\n",
" <td>6.768012</td>\n",
" <td>6.937238</td>\n",
" <td>7.399257</td>\n",
" <td>6.863133</td>\n",
" <td>6.620010</td>\n",
" <td>6.248286</td>\n",
" <td>6.748421</td>\n",
" <td>7.307337</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SGSM3\\214779_s_at</th>\n",
" <td>6.085620</td>\n",
" <td>6.222101</td>\n",
" <td>6.369159</td>\n",
" <td>6.973898</td>\n",
" <td>6.480099</td>\n",
" <td>6.975206</td>\n",
" <td>5.502980</td>\n",
" <td>7.249825</td>\n",
" <td>0.897953</td>\n",
" <td>6.538965</td>\n",
" <td>...</td>\n",
" <td>5.941064</td>\n",
" <td>5.356978</td>\n",
" <td>6.027309</td>\n",
" <td>6.476560</td>\n",
" <td>5.856627</td>\n",
" <td>6.019471</td>\n",
" <td>6.557572</td>\n",
" <td>6.265962</td>\n",
" <td>6.514209</td>\n",
" <td>6.515731</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100508009\\231516_at</th>\n",
" <td>0.096289</td>\n",
" <td>1.096255</td>\n",
" <td>0.515016</td>\n",
" <td>3.825775</td>\n",
" <td>0.814985</td>\n",
" <td>1.810900</td>\n",
" <td>0.980647</td>\n",
" <td>0.710578</td>\n",
" <td>-0.739851</td>\n",
" <td>1.229330</td>\n",
" <td>...</td>\n",
" <td>2.959913</td>\n",
" <td>0.891940</td>\n",
" <td>2.153809</td>\n",
" <td>1.315792</td>\n",
" <td>0.238775</td>\n",
" <td>2.161891</td>\n",
" <td>-0.271548</td>\n",
" <td>3.107577</td>\n",
" <td>1.807009</td>\n",
" <td>1.288778</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ASCL3\\221161_at</th>\n",
" <td>1.922221</td>\n",
" <td>2.277330</td>\n",
" <td>0.649220</td>\n",
" <td>0.826160</td>\n",
" <td>1.251083</td>\n",
" <td>1.344811</td>\n",
" <td>1.827514</td>\n",
" <td>2.201690</td>\n",
" <td>-0.836759</td>\n",
" <td>0.725732</td>\n",
" <td>...</td>\n",
" <td>1.347926</td>\n",
" <td>2.185626</td>\n",
" <td>3.873656</td>\n",
" <td>2.863080</td>\n",
" <td>1.878725</td>\n",
" <td>3.481389</td>\n",
" <td>1.936025</td>\n",
" <td>1.229871</td>\n",
" <td>2.364402</td>\n",
" <td>4.689098</td>\n",
" </tr>\n",
" <tr>\n",
" <th>DALRD3\\221934_s_at</th>\n",
" <td>6.547675</td>\n",
" <td>6.662049</td>\n",
" <td>7.235248</td>\n",
" <td>7.967169</td>\n",
" <td>6.343070</td>\n",
" <td>6.658169</td>\n",
" <td>5.783467</td>\n",
" <td>8.331239</td>\n",
" <td>-0.712632</td>\n",
" <td>6.685029</td>\n",
" <td>...</td>\n",
" <td>6.582208</td>\n",
" <td>5.760176</td>\n",
" <td>6.454429</td>\n",
" <td>6.624623</td>\n",
" <td>6.385816</td>\n",
" <td>6.535386</td>\n",
" <td>5.936365</td>\n",
" <td>6.064210</td>\n",
" <td>6.503974</td>\n",
" <td>7.208312</td>\n",
" </tr>\n",
" <tr>\n",
" <th>DAPK2\\206324_s_at</th>\n",
" <td>6.076309</td>\n",
" <td>5.018585</td>\n",
" <td>6.288045</td>\n",
" <td>5.766722</td>\n",
" <td>6.336778</td>\n",
" <td>6.174706</td>\n",
" <td>5.848886</td>\n",
" <td>7.684854</td>\n",
" <td>1.262565</td>\n",
" <td>6.172818</td>\n",
" <td>...</td>\n",
" <td>6.513636</td>\n",
" <td>5.814207</td>\n",
" <td>6.558405</td>\n",
" <td>6.266966</td>\n",
" <td>6.625050</td>\n",
" <td>5.898878</td>\n",
" <td>6.420723</td>\n",
" <td>5.547712</td>\n",
" <td>6.288178</td>\n",
" <td>6.460918</td>\n",
" </tr>\n",
" <tr>\n",
" <th>NUP155\\206550_s_at</th>\n",
" <td>5.682739</td>\n",
" <td>5.818999</td>\n",
" <td>5.499269</td>\n",
" <td>5.766245</td>\n",
" <td>5.763932</td>\n",
" <td>5.789187</td>\n",
" <td>5.309784</td>\n",
" <td>6.276657</td>\n",
" <td>-1.643888</td>\n",
" <td>5.657866</td>\n",
" <td>...</td>\n",
" <td>5.756418</td>\n",
" <td>5.360438</td>\n",
" <td>5.776744</td>\n",
" <td>5.280626</td>\n",
" <td>5.654484</td>\n",
" <td>5.879899</td>\n",
" <td>5.116348</td>\n",
" <td>5.056328</td>\n",
" <td>5.814168</td>\n",
" <td>5.992225</td>\n",
" </tr>\n",
" <tr>\n",
" <th>TMF1\\215855_s_at</th>\n",
" <td>6.156229</td>\n",
" <td>6.369199</td>\n",
" <td>6.536076</td>\n",
" <td>7.205373</td>\n",
" <td>6.901917</td>\n",
" <td>6.290164</td>\n",
" <td>5.627009</td>\n",
" <td>7.228078</td>\n",
" <td>1.701886</td>\n",
" <td>6.290089</td>\n",
" <td>...</td>\n",
" <td>7.134426</td>\n",
" <td>6.639760</td>\n",
" <td>7.250412</td>\n",
" <td>6.137225</td>\n",
" <td>7.059755</td>\n",
" <td>6.960465</td>\n",
" <td>6.188907</td>\n",
" <td>5.935240</td>\n",
" <td>6.379973</td>\n",
" <td>7.085053</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100505584\\216336_x_at</th>\n",
" <td>8.288312</td>\n",
" <td>9.388792</td>\n",
" <td>9.709828</td>\n",
" <td>9.903338</td>\n",
" <td>8.082910</td>\n",
" <td>9.816838</td>\n",
" <td>11.912272</td>\n",
" <td>10.181450</td>\n",
" <td>-1.755205</td>\n",
" <td>8.662366</td>\n",
" <td>...</td>\n",
" <td>8.983002</td>\n",
" <td>8.092414</td>\n",
" <td>9.432051</td>\n",
" <td>8.614206</td>\n",
" <td>10.255855</td>\n",
" <td>9.316582</td>\n",
" <td>9.096483</td>\n",
" <td>10.313688</td>\n",
" <td>9.599377</td>\n",
" <td>9.511547</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ARID1B\\1566990_x_at</th>\n",
" <td>4.844024</td>\n",
" <td>5.269897</td>\n",
" <td>6.362356</td>\n",
" <td>6.720921</td>\n",
" <td>7.043224</td>\n",
" <td>6.658440</td>\n",
" <td>3.971847</td>\n",
" <td>7.161868</td>\n",
" <td>-1.014234</td>\n",
" <td>6.987150</td>\n",
" <td>...</td>\n",
" <td>6.915891</td>\n",
" <td>3.020854</td>\n",
" <td>7.189617</td>\n",
" <td>6.719129</td>\n",
" <td>5.611276</td>\n",
" <td>6.995089</td>\n",
" <td>6.711302</td>\n",
" <td>6.026610</td>\n",
" <td>6.801663</td>\n",
" <td>6.861558</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100287105\\1570171_at</th>\n",
" <td>4.233727</td>\n",
" <td>-0.677248</td>\n",
" <td>4.755833</td>\n",
" <td>-0.291195</td>\n",
" <td>4.693548</td>\n",
" <td>4.466510</td>\n",
" <td>2.796884</td>\n",
" <td>0.496319</td>\n",
" <td>-2.507304</td>\n",
" <td>4.189840</td>\n",
" <td>...</td>\n",
" <td>4.805323</td>\n",
" <td>3.401112</td>\n",
" <td>5.732815</td>\n",
" <td>4.001865</td>\n",
" <td>3.472046</td>\n",
" <td>3.889658</td>\n",
" <td>3.857832</td>\n",
" <td>4.390365</td>\n",
" <td>4.126296</td>\n",
" <td>4.692935</td>\n",
" </tr>\n",
" <tr>\n",
" <th>UTRN\\225093_at</th>\n",
" <td>9.833749</td>\n",
" <td>9.269433</td>\n",
" <td>9.563961</td>\n",
" <td>9.706814</td>\n",
" <td>9.910094</td>\n",
" <td>9.638782</td>\n",
" <td>9.227060</td>\n",
" <td>10.398060</td>\n",
" <td>1.566776</td>\n",
" <td>9.608661</td>\n",
" <td>...</td>\n",
" <td>10.277857</td>\n",
" <td>9.241731</td>\n",
" <td>10.015582</td>\n",
" <td>9.443418</td>\n",
" <td>10.313541</td>\n",
" <td>9.934789</td>\n",
" <td>9.209356</td>\n",
" <td>9.069648</td>\n",
" <td>9.137393</td>\n",
" <td>10.477890</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HIST3H3\\208572_at</th>\n",
" <td>1.768743</td>\n",
" <td>-1.215312</td>\n",
" <td>1.763084</td>\n",
" <td>0.591574</td>\n",
" <td>1.286769</td>\n",
" <td>1.156630</td>\n",
" <td>-0.589066</td>\n",
" <td>2.876366</td>\n",
" <td>1.766430</td>\n",
" <td>-0.396998</td>\n",
" <td>...</td>\n",
" <td>1.981359</td>\n",
" <td>-0.848611</td>\n",
" <td>0.938083</td>\n",
" <td>2.529259</td>\n",
" <td>0.210688</td>\n",
" <td>4.452576</td>\n",
" <td>2.046432</td>\n",
" <td>-0.111016</td>\n",
" <td>0.831756</td>\n",
" <td>0.302477</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ZNF316\\227170_at</th>\n",
" <td>4.836979</td>\n",
" <td>4.754369</td>\n",
" <td>5.339087</td>\n",
" <td>6.241935</td>\n",
" <td>5.000189</td>\n",
" <td>5.288632</td>\n",
" <td>3.610665</td>\n",
" <td>6.449428</td>\n",
" <td>2.224784</td>\n",
" <td>4.808720</td>\n",
" <td>...</td>\n",
" <td>5.483455</td>\n",
" <td>4.643371</td>\n",
" <td>5.596381</td>\n",
" <td>5.228653</td>\n",
" <td>5.093509</td>\n",
" <td>4.529546</td>\n",
" <td>4.899219</td>\n",
" <td>5.149950</td>\n",
" <td>4.447850</td>\n",
" <td>5.308212</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ETV6\\205585_at</th>\n",
" <td>4.575185</td>\n",
" <td>4.743413</td>\n",
" <td>4.879990</td>\n",
" <td>5.281887</td>\n",
" <td>5.425627</td>\n",
" <td>4.660284</td>\n",
" <td>4.686304</td>\n",
" <td>5.703884</td>\n",
" <td>1.654825</td>\n",
" <td>4.405141</td>\n",
" <td>...</td>\n",
" <td>4.634884</td>\n",
" <td>4.554270</td>\n",
" <td>5.222492</td>\n",
" <td>5.008505</td>\n",
" <td>4.727093</td>\n",
" <td>4.823994</td>\n",
" <td>5.700418</td>\n",
" <td>4.969933</td>\n",
" <td>5.274616</td>\n",
" <td>4.586272</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC400550\\243059_at</th>\n",
" <td>5.382072</td>\n",
" <td>2.839498</td>\n",
" <td>5.541248</td>\n",
" <td>5.309984</td>\n",
" <td>3.720858</td>\n",
" <td>5.915354</td>\n",
" <td>4.588151</td>\n",
" <td>6.245929</td>\n",
" <td>-0.320133</td>\n",
" <td>5.678018</td>\n",
" <td>...</td>\n",
" <td>3.835964</td>\n",
" <td>4.854165</td>\n",
" <td>4.917408</td>\n",
" <td>6.209835</td>\n",
" <td>6.165832</td>\n",
" <td>5.456901</td>\n",
" <td>4.670619</td>\n",
" <td>4.239658</td>\n",
" <td>5.598508</td>\n",
" <td>5.056883</td>\n",
" </tr>\n",
" <tr>\n",
" <th>B3GAT2\\234146_at</th>\n",
" <td>-0.386897</td>\n",
" <td>0.987605</td>\n",
" <td>4.152630</td>\n",
" <td>0.334202</td>\n",
" <td>1.905255</td>\n",
" <td>1.575458</td>\n",
" <td>1.176240</td>\n",
" <td>1.627682</td>\n",
" <td>0.125400</td>\n",
" <td>1.377540</td>\n",
" <td>...</td>\n",
" <td>3.713476</td>\n",
" <td>2.656606</td>\n",
" <td>2.477006</td>\n",
" <td>1.141858</td>\n",
" <td>0.080180</td>\n",
" <td>3.536140</td>\n",
" <td>0.672525</td>\n",
" <td>0.800894</td>\n",
" <td>1.226626</td>\n",
" <td>-0.418888</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HMGB4\\230473_s_at</th>\n",
" <td>0.768832</td>\n",
" <td>2.292431</td>\n",
" <td>1.270350</td>\n",
" <td>0.530261</td>\n",
" <td>2.196421</td>\n",
" <td>0.710649</td>\n",
" <td>3.439078</td>\n",
" <td>1.771387</td>\n",
" <td>1.225337</td>\n",
" <td>1.973435</td>\n",
" <td>...</td>\n",
" <td>1.142165</td>\n",
" <td>1.185105</td>\n",
" <td>4.201320</td>\n",
" <td>3.796577</td>\n",
" <td>3.935149</td>\n",
" <td>2.021405</td>\n",
" <td>3.901861</td>\n",
" <td>0.221753</td>\n",
" <td>1.330432</td>\n",
" <td>2.412188</td>\n",
" </tr>\n",
" <tr>\n",
" <th>CMTM6\\217947_at</th>\n",
" <td>11.015812</td>\n",
" <td>10.862289</td>\n",
" <td>10.657202</td>\n",
" <td>10.861451</td>\n",
" <td>11.117546</td>\n",
" <td>10.326677</td>\n",
" <td>10.614084</td>\n",
" <td>11.129753</td>\n",
" <td>-0.803652</td>\n",
" <td>9.888813</td>\n",
" <td>...</td>\n",
" <td>10.930656</td>\n",
" <td>10.071798</td>\n",
" <td>11.387102</td>\n",
" <td>10.178316</td>\n",
" <td>11.016843</td>\n",
" <td>10.761393</td>\n",
" <td>10.173565</td>\n",
" <td>10.378219</td>\n",
" <td>10.059845</td>\n",
" <td>11.053553</td>\n",
" </tr>\n",
" <tr>\n",
" <th>BRAP\\209922_at</th>\n",
" <td>4.675726</td>\n",
" <td>4.753610</td>\n",
" <td>2.947975</td>\n",
" <td>4.963201</td>\n",
" <td>4.252575</td>\n",
" <td>5.015266</td>\n",
" <td>3.479696</td>\n",
" <td>5.331078</td>\n",
" <td>0.148296</td>\n",
" <td>4.329633</td>\n",
" <td>...</td>\n",
" <td>4.418021</td>\n",
" <td>0.507516</td>\n",
" <td>3.151500</td>\n",
" <td>4.509461</td>\n",
" <td>4.517975</td>\n",
" <td>4.317355</td>\n",
" <td>3.179204</td>\n",
" <td>4.385003</td>\n",
" <td>4.397837</td>\n",
" <td>5.448458</td>\n",
" </tr>\n",
" <tr>\n",
" <th>BARD1\\205345_at</th>\n",
" <td>6.710517</td>\n",
" <td>7.206467</td>\n",
" <td>6.289503</td>\n",
" <td>6.951098</td>\n",
" <td>7.049707</td>\n",
" <td>6.193521</td>\n",
" <td>5.579328</td>\n",
" <td>7.003006</td>\n",
" <td>-0.610828</td>\n",
" <td>5.801891</td>\n",
" <td>...</td>\n",
" <td>7.624445</td>\n",
" <td>5.735102</td>\n",
" <td>7.444344</td>\n",
" <td>5.718608</td>\n",
" <td>6.613499</td>\n",
" <td>6.629858</td>\n",
" <td>5.432485</td>\n",
" <td>5.495951</td>\n",
" <td>5.855873</td>\n",
" <td>7.085850</td>\n",
" </tr>\n",
" <tr>\n",
" <th>MR1\\207565_s_at</th>\n",
" <td>6.637055</td>\n",
" <td>5.254945</td>\n",
" <td>6.448450</td>\n",
" <td>6.319414</td>\n",
" <td>5.230975</td>\n",
" <td>5.953328</td>\n",
" <td>5.426516</td>\n",
" <td>6.940167</td>\n",
" <td>-2.418720</td>\n",
" <td>6.156089</td>\n",
" <td>...</td>\n",
" <td>5.215585</td>\n",
" <td>5.203107</td>\n",
" <td>6.598879</td>\n",
" <td>6.072202</td>\n",
" <td>6.262719</td>\n",
" <td>6.137137</td>\n",
" <td>6.315622</td>\n",
" <td>6.195515</td>\n",
" <td>6.094489</td>\n",
" <td>5.978122</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SORT1\\212797_at</th>\n",
" <td>7.184548</td>\n",
" <td>2.766555</td>\n",
" <td>5.831305</td>\n",
" <td>6.176744</td>\n",
" <td>5.082562</td>\n",
" <td>7.390246</td>\n",
" <td>5.628421</td>\n",
" <td>7.536076</td>\n",
" <td>-0.055522</td>\n",
" <td>6.785197</td>\n",
" <td>...</td>\n",
" <td>5.026180</td>\n",
" <td>5.021151</td>\n",
" <td>6.463953</td>\n",
" <td>6.556249</td>\n",
" <td>7.355034</td>\n",
" <td>6.665094</td>\n",
" <td>5.903407</td>\n",
" <td>6.181027</td>\n",
" <td>6.315383</td>\n",
" <td>6.688852</td>\n",
" </tr>\n",
" <tr>\n",
" <th>FLJ31485\\243351_at</th>\n",
" <td>5.210751</td>\n",
" <td>4.899064</td>\n",
" <td>4.497050</td>\n",
" <td>5.087157</td>\n",
" <td>5.677080</td>\n",
" <td>4.700828</td>\n",
" <td>4.613101</td>\n",
" <td>4.765312</td>\n",
" <td>3.323658</td>\n",
" <td>4.587989</td>\n",
" <td>...</td>\n",
" <td>5.163277</td>\n",
" <td>4.226216</td>\n",
" <td>5.596187</td>\n",
" <td>4.388465</td>\n",
" <td>3.612706</td>\n",
" <td>4.759539</td>\n",
" <td>4.475967</td>\n",
" <td>4.051703</td>\n",
" <td>4.583555</td>\n",
" <td>4.557226</td>\n",
" </tr>\n",
" <tr>\n",
" <th>BPI\\205557_at</th>\n",
" <td>2.630375</td>\n",
" <td>1.126458</td>\n",
" <td>4.039314</td>\n",
" <td>3.758495</td>\n",
" <td>1.021863</td>\n",
" <td>4.347935</td>\n",
" <td>4.324141</td>\n",
" <td>3.819515</td>\n",
" <td>1.737929</td>\n",
" <td>4.419694</td>\n",
" <td>...</td>\n",
" <td>0.860836</td>\n",
" <td>3.239855</td>\n",
" <td>2.144037</td>\n",
" <td>0.549590</td>\n",
" <td>3.909869</td>\n",
" <td>2.452711</td>\n",
" <td>2.145231</td>\n",
" <td>5.314164</td>\n",
" <td>1.435842</td>\n",
" <td>4.217409</td>\n",
" </tr>\n",
" <tr>\n",
" <th>CECR3\\1564352_at</th>\n",
" <td>2.728809</td>\n",
" <td>3.588373</td>\n",
" <td>3.907554</td>\n",
" <td>3.747441</td>\n",
" <td>4.007599</td>\n",
" <td>4.303079</td>\n",
" <td>2.497137</td>\n",
" <td>4.297177</td>\n",
" <td>0.328388</td>\n",
" <td>4.361979</td>\n",
" <td>...</td>\n",
" <td>4.470934</td>\n",
" <td>4.405128</td>\n",
" <td>2.572625</td>\n",
" <td>3.996723</td>\n",
" <td>4.119672</td>\n",
" <td>4.514905</td>\n",
" <td>4.044753</td>\n",
" <td>3.865632</td>\n",
" <td>3.683932</td>\n",
" <td>3.858588</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>42449 rows × 55 columns</p>\n",
"</div>"
],
"text/plain": [
" GSE8581GSM213034 GSE8581GSM212811 \\\n",
"KIAA1377\\235956_at 6.461792 7.461758 \n",
"ZNF358\\226260_x_at 4.969012 1.053695 \n",
"GPR135\\214503_x_at 0.313037 -1.114216 \n",
"GPATCH2\\242224_at 4.989094 4.451818 \n",
"RPL24\\214143_x_at 12.746451 12.414838 \n",
"PALM2\\1554640_at 4.713311 4.580507 \n",
"LOC339316\\242084_at 0.759616 0.678216 \n",
"FECH\\203115_at 5.924822 5.616725 \n",
"KCNJ9\\207527_at 3.415177 2.037192 \n",
"C21orf96\\220918_at 5.862719 5.615584 \n",
"SAT2\\225272_at 8.531444 8.361009 \n",
"EHD1\\209038_s_at 4.654092 5.696230 \n",
"CBLB\\208348_s_at 2.811568 -1.355841 \n",
"C20orf85\\229542_at 6.652214 7.913548 \n",
"UGGT1\\218257_s_at 5.788636 5.553766 \n",
"LOC283585\\1561442_at 2.861265 2.867798 \n",
"EMP2\\204975_at 11.154514 10.251210 \n",
"LHFP\\218656_s_at 9.192811 9.300302 \n",
"SNCAIP\\237834_at 3.468440 1.408119 \n",
"RDH8\\220683_at 3.984535 4.318512 \n",
"SRSF4\\239512_at 7.591979 5.857429 \n",
"ACTB\\213867_x_at 13.404822 12.845100 \n",
"FAM182B\\215487_x_at 1.759795 0.421856 \n",
"C6orf108\\213871_s_at 3.582701 1.259200 \n",
"CSRNP2\\225042_s_at 6.374174 4.883411 \n",
"SLCO2B1\\203473_at 10.034813 8.756970 \n",
"MYNN\\237510_at 2.361996 0.114700 \n",
"NAP1L1\\208752_x_at 10.628446 10.585366 \n",
"ADAM28\\205997_at 5.450776 6.641620 \n",
"LOC100507248\\235236_at 0.841828 3.184030 \n",
"PHF8\\238837_at 0.414558 0.418255 \n",
"C9orf96\\1554787_at 4.105762 1.087877 \n",
"TNPO2\\210585_s_at 4.113917 0.407559 \n",
"FLJ31485\\239569_at 3.371838 2.244808 \n",
"PUM1\\201164_s_at 9.192882 8.685846 \n",
"COX4I1\\202698_x_at 11.424980 11.025444 \n",
"IZUMO4\\215734_at 5.042977 2.857635 \n",
"TPSAB1\\216485_s_at 0.137189 2.176741 \n",
"LMAN1L\\220420_at 1.562934 3.100598 \n",
"LY6K\\223687_s_at 1.228997 3.534535 \n",
"ACAD10\\238655_at 4.785132 1.079429 \n",
"TIMM22\\219184_x_at 6.169121 5.517953 \n",
"HUS1\\217618_x_at 5.018104 4.675059 \n",
"EPHA7\\206852_at 3.069138 3.238351 \n",
"CSH1\\208069_x_at 1.359319 0.969477 \n",
"FMNL2\\242665_at 5.583281 4.859274 \n",
"PUS3\\221277_s_at 6.631467 6.873272 \n",
"CELF4\\231220_at 0.441579 -0.481415 \n",
"RBM6\\228030_at 9.486984 9.160928 \n",
"AVIL\\233333_x_at 5.856667 5.921548 \n",
"... ... ... \n",
"MON1B\\233557_s_at 7.322334 5.598157 \n",
"CLLU1\\1558185_at 3.180862 3.434628 \n",
"KTN1\\214709_s_at 9.996389 9.792563 \n",
"KRTAP4-7\\216810_at 2.492058 1.778827 \n",
"RBKS\\219222_at 6.212774 5.976840 \n",
"LOC100506621\\227061_at 7.323550 7.469943 \n",
"CCDC67\\1554071_at 1.965267 2.750519 \n",
"MCM9\\219673_at 6.303923 5.747465 \n",
"LOC730101\\213248_at 5.458103 6.042692 \n",
"LOC100508546\\244037_at 4.314747 4.632012 \n",
"RNPS1\\200060_s_at 9.180869 9.034972 \n",
"C8orf74\\1569246_a_at 3.316081 1.549364 \n",
"UTP14C\\203614_at 8.437311 7.923203 \n",
"RHEB\\201452_at 4.676200 1.578282 \n",
"CXCL16\\223454_at 9.465360 8.289337 \n",
"PSPC1\\218371_s_at 7.101902 6.961612 \n",
"SIK3\\213034_at 7.888189 7.736754 \n",
"ACOT9\\221641_s_at 9.054124 8.092091 \n",
"KIAA1661\\215943_at 3.452543 2.797194 \n",
"STEAP2\\225871_at 6.958019 8.671654 \n",
"AKAP5\\207800_at 1.097725 1.830588 \n",
"C1orf57\\223272_s_at 6.872743 5.970815 \n",
"C7orf30\\226385_s_at 9.253008 9.173635 \n",
"BAX\\208478_s_at 5.946710 5.331426 \n",
"MAN1C1\\218918_at 6.990875 6.941024 \n",
"SGSM3\\214779_s_at 6.085620 6.222101 \n",
"LOC100508009\\231516_at 0.096289 1.096255 \n",
"ASCL3\\221161_at 1.922221 2.277330 \n",
"DALRD3\\221934_s_at 6.547675 6.662049 \n",
"DAPK2\\206324_s_at 6.076309 5.018585 \n",
"NUP155\\206550_s_at 5.682739 5.818999 \n",
"TMF1\\215855_s_at 6.156229 6.369199 \n",
"LOC100505584\\216336_x_at 8.288312 9.388792 \n",
"ARID1B\\1566990_x_at 4.844024 5.269897 \n",
"LOC100287105\\1570171_at 4.233727 -0.677248 \n",
"UTRN\\225093_at 9.833749 9.269433 \n",
"HIST3H3\\208572_at 1.768743 -1.215312 \n",
"ZNF316\\227170_at 4.836979 4.754369 \n",
"ETV6\\205585_at 4.575185 4.743413 \n",
"LOC400550\\243059_at 5.382072 2.839498 \n",
"B3GAT2\\234146_at -0.386897 0.987605 \n",
"HMGB4\\230473_s_at 0.768832 2.292431 \n",
"CMTM6\\217947_at 11.015812 10.862289 \n",
"BRAP\\209922_at 4.675726 4.753610 \n",
"BARD1\\205345_at 6.710517 7.206467 \n",
"MR1\\207565_s_at 6.637055 5.254945 \n",
"SORT1\\212797_at 7.184548 2.766555 \n",
"FLJ31485\\243351_at 5.210751 4.899064 \n",
"BPI\\205557_at 2.630375 1.126458 \n",
"CECR3\\1564352_at 2.728809 3.588373 \n",
"\n",
" GSE8581GSM213036 GSE8581GSM212075 \\\n",
"KIAA1377\\235956_at 6.907191 7.775558 \n",
"ZNF358\\226260_x_at 5.064348 4.766791 \n",
"GPR135\\214503_x_at 0.569997 -0.156695 \n",
"GPATCH2\\242224_at 4.066089 4.839037 \n",
"RPL24\\214143_x_at 12.393632 12.335932 \n",
"PALM2\\1554640_at 4.187253 5.226393 \n",
"LOC339316\\242084_at 3.717528 -0.063451 \n",
"FECH\\203115_at 4.892148 5.171583 \n",
"KCNJ9\\207527_at 3.383345 3.765651 \n",
"C21orf96\\220918_at 6.010954 6.295001 \n",
"SAT2\\225272_at 8.189889 8.728519 \n",
"EHD1\\209038_s_at 5.233359 5.462065 \n",
"CBLB\\208348_s_at 1.747310 2.343664 \n",
"C20orf85\\229542_at 7.191395 8.238376 \n",
"UGGT1\\218257_s_at 5.148186 6.058695 \n",
"LOC283585\\1561442_at 4.049178 1.020051 \n",
"EMP2\\204975_at 10.557148 11.385383 \n",
"LHFP\\218656_s_at 9.506220 9.353908 \n",
"SNCAIP\\237834_at 3.229285 2.280220 \n",
"RDH8\\220683_at 0.107701 4.391073 \n",
"SRSF4\\239512_at 7.502020 8.401899 \n",
"ACTB\\213867_x_at 13.204111 13.159971 \n",
"FAM182B\\215487_x_at 4.997703 1.714052 \n",
"C6orf108\\213871_s_at 2.048599 2.109661 \n",
"CSRNP2\\225042_s_at 6.401555 6.514329 \n",
"SLCO2B1\\203473_at 9.486851 9.691714 \n",
"MYNN\\237510_at 3.387004 2.883904 \n",
"NAP1L1\\208752_x_at 10.177594 10.648825 \n",
"ADAM28\\205997_at 4.300285 6.839683 \n",
"LOC100507248\\235236_at 1.062971 1.479386 \n",
"PHF8\\238837_at 0.683068 -0.057428 \n",
"C9orf96\\1554787_at 1.965241 0.014298 \n",
"TNPO2\\210585_s_at 2.646727 4.812313 \n",
"FLJ31485\\239569_at 4.399171 3.569661 \n",
"PUM1\\201164_s_at 8.694556 8.958501 \n",
"COX4I1\\202698_x_at 10.975160 11.094902 \n",
"IZUMO4\\215734_at 4.268292 4.661282 \n",
"TPSAB1\\216485_s_at 1.948201 4.195206 \n",
"LMAN1L\\220420_at 1.747254 3.675906 \n",
"LY6K\\223687_s_at 3.803702 4.598181 \n",
"ACAD10\\238655_at 4.897531 1.068464 \n",
"TIMM22\\219184_x_at 6.243324 6.358511 \n",
"HUS1\\217618_x_at 6.151751 5.439500 \n",
"EPHA7\\206852_at 3.662547 -0.638656 \n",
"CSH1\\208069_x_at 1.082062 0.112980 \n",
"FMNL2\\242665_at 6.557625 5.519202 \n",
"PUS3\\221277_s_at 6.322101 7.021946 \n",
"CELF4\\231220_at 2.454702 2.611196 \n",
"RBM6\\228030_at 10.017463 9.410869 \n",
"AVIL\\233333_x_at 7.078343 6.954941 \n",
"... ... ... \n",
"MON1B\\233557_s_at 7.301825 7.463622 \n",
"CLLU1\\1558185_at 1.344834 3.800320 \n",
"KTN1\\214709_s_at 10.114302 9.761053 \n",
"KRTAP4-7\\216810_at 2.818088 0.879745 \n",
"RBKS\\219222_at 5.731031 6.378312 \n",
"LOC100506621\\227061_at 9.200810 7.576832 \n",
"CCDC67\\1554071_at 0.020598 3.295987 \n",
"MCM9\\219673_at 6.153033 6.292412 \n",
"LOC730101\\213248_at 5.830443 5.714144 \n",
"LOC100508546\\244037_at 4.600192 4.657777 \n",
"RNPS1\\200060_s_at 9.006116 9.652415 \n",
"C8orf74\\1569246_a_at 2.521832 4.597054 \n",
"UTP14C\\203614_at 7.907924 8.131415 \n",
"RHEB\\201452_at 4.372318 3.111474 \n",
"CXCL16\\223454_at 9.233644 9.871523 \n",
"PSPC1\\218371_s_at 7.179372 7.431514 \n",
"SIK3\\213034_at 7.553514 7.753431 \n",
"ACOT9\\221641_s_at 8.246622 8.634089 \n",
"KIAA1661\\215943_at 3.073855 0.238921 \n",
"STEAP2\\225871_at 7.542428 7.343310 \n",
"AKAP5\\207800_at 1.652087 1.086485 \n",
"C1orf57\\223272_s_at 6.643149 6.758743 \n",
"C7orf30\\226385_s_at 8.618015 9.345833 \n",
"BAX\\208478_s_at 5.553677 5.729118 \n",
"MAN1C1\\218918_at 6.985261 6.772004 \n",
"SGSM3\\214779_s_at 6.369159 6.973898 \n",
"LOC100508009\\231516_at 0.515016 3.825775 \n",
"ASCL3\\221161_at 0.649220 0.826160 \n",
"DALRD3\\221934_s_at 7.235248 7.967169 \n",
"DAPK2\\206324_s_at 6.288045 5.766722 \n",
"NUP155\\206550_s_at 5.499269 5.766245 \n",
"TMF1\\215855_s_at 6.536076 7.205373 \n",
"LOC100505584\\216336_x_at 9.709828 9.903338 \n",
"ARID1B\\1566990_x_at 6.362356 6.720921 \n",
"LOC100287105\\1570171_at 4.755833 -0.291195 \n",
"UTRN\\225093_at 9.563961 9.706814 \n",
"HIST3H3\\208572_at 1.763084 0.591574 \n",
"ZNF316\\227170_at 5.339087 6.241935 \n",
"ETV6\\205585_at 4.879990 5.281887 \n",
"LOC400550\\243059_at 5.541248 5.309984 \n",
"B3GAT2\\234146_at 4.152630 0.334202 \n",
"HMGB4\\230473_s_at 1.270350 0.530261 \n",
"CMTM6\\217947_at 10.657202 10.861451 \n",
"BRAP\\209922_at 2.947975 4.963201 \n",
"BARD1\\205345_at 6.289503 6.951098 \n",
"MR1\\207565_s_at 6.448450 6.319414 \n",
"SORT1\\212797_at 5.831305 6.176744 \n",
"FLJ31485\\243351_at 4.497050 5.087157 \n",
"BPI\\205557_at 4.039314 3.758495 \n",
"CECR3\\1564352_at 3.907554 3.747441 \n",
"\n",
" GSE8581GSM211008 GSE8581GSM210090 \\\n",
"KIAA1377\\235956_at 7.308785 6.286654 \n",
"ZNF358\\226260_x_at 3.559235 4.967538 \n",
"GPR135\\214503_x_at 0.268782 0.108009 \n",
"GPATCH2\\242224_at 4.612494 4.843898 \n",
"RPL24\\214143_x_at 12.488262 12.386385 \n",
"PALM2\\1554640_at 2.517850 3.331075 \n",
"LOC339316\\242084_at 2.928876 0.940558 \n",
"FECH\\203115_at 5.930726 5.670852 \n",
"KCNJ9\\207527_at 3.043836 4.304745 \n",
"C21orf96\\220918_at 4.157214 4.917064 \n",
"SAT2\\225272_at 7.830052 8.680068 \n",
"EHD1\\209038_s_at 4.909850 5.028790 \n",
"CBLB\\208348_s_at 3.683607 -0.044488 \n",
"C20orf85\\229542_at 5.263647 6.728356 \n",
"UGGT1\\218257_s_at 5.965759 6.196871 \n",
"LOC283585\\1561442_at 4.728040 4.182049 \n",
"EMP2\\204975_at 11.230987 11.683977 \n",
"LHFP\\218656_s_at 9.686849 9.403093 \n",
"SNCAIP\\237834_at 2.810227 2.852077 \n",
"RDH8\\220683_at 3.984945 4.485176 \n",
"SRSF4\\239512_at 8.216115 7.893508 \n",
"ACTB\\213867_x_at 12.755121 12.987085 \n",
"FAM182B\\215487_x_at 3.881694 4.046220 \n",
"C6orf108\\213871_s_at 3.604059 3.220994 \n",
"CSRNP2\\225042_s_at 6.049038 5.922999 \n",
"SLCO2B1\\203473_at 8.997532 9.316754 \n",
"MYNN\\237510_at 4.976735 3.417407 \n",
"NAP1L1\\208752_x_at 10.851038 10.756323 \n",
"ADAM28\\205997_at 5.465109 5.555887 \n",
"LOC100507248\\235236_at 1.279673 -1.013605 \n",
"PHF8\\238837_at 0.478299 0.191297 \n",
"C9orf96\\1554787_at 4.360371 4.244400 \n",
"TNPO2\\210585_s_at 3.139695 4.940749 \n",
"FLJ31485\\239569_at 2.099006 5.009110 \n",
"PUM1\\201164_s_at 9.190432 8.840312 \n",
"COX4I1\\202698_x_at 10.266833 11.072702 \n",
"IZUMO4\\215734_at 4.639140 4.592122 \n",
"TPSAB1\\216485_s_at 2.251562 0.251071 \n",
"LMAN1L\\220420_at 3.429080 1.925282 \n",
"LY6K\\223687_s_at 3.881948 1.130984 \n",
"ACAD10\\238655_at 3.974392 5.051342 \n",
"TIMM22\\219184_x_at 6.519636 5.950811 \n",
"HUS1\\217618_x_at 5.783855 6.387462 \n",
"EPHA7\\206852_at 3.145749 2.637562 \n",
"CSH1\\208069_x_at 1.229982 1.225509 \n",
"FMNL2\\242665_at 6.182331 5.753663 \n",
"PUS3\\221277_s_at 6.664013 6.887208 \n",
"CELF4\\231220_at 0.427831 2.381018 \n",
"RBM6\\228030_at 9.978954 8.680039 \n",
"AVIL\\233333_x_at 7.159518 6.541760 \n",
"... ... ... \n",
"MON1B\\233557_s_at 6.327718 6.466811 \n",
"CLLU1\\1558185_at 2.806260 -0.134157 \n",
"KTN1\\214709_s_at 10.761277 10.352209 \n",
"KRTAP4-7\\216810_at 2.604634 2.112997 \n",
"RBKS\\219222_at 5.044739 4.772419 \n",
"LOC100506621\\227061_at 7.448273 6.004852 \n",
"CCDC67\\1554071_at 0.489317 -0.952302 \n",
"MCM9\\219673_at 6.461627 6.652888 \n",
"LOC730101\\213248_at 6.086276 5.952103 \n",
"LOC100508546\\244037_at 6.033800 3.933337 \n",
"RNPS1\\200060_s_at 8.701539 9.218159 \n",
"C8orf74\\1569246_a_at 5.367626 4.720995 \n",
"UTP14C\\203614_at 8.309217 8.235052 \n",
"RHEB\\201452_at 0.485128 2.154006 \n",
"CXCL16\\223454_at 8.590482 9.214773 \n",
"PSPC1\\218371_s_at 7.177051 7.279490 \n",
"SIK3\\213034_at 7.962983 7.863926 \n",
"ACOT9\\221641_s_at 7.678487 8.523825 \n",
"KIAA1661\\215943_at 0.288016 2.898096 \n",
"STEAP2\\225871_at 6.991034 6.901712 \n",
"AKAP5\\207800_at 0.702108 1.539263 \n",
"C1orf57\\223272_s_at 6.745412 6.706544 \n",
"C7orf30\\226385_s_at 8.935483 9.336312 \n",
"BAX\\208478_s_at 3.767771 6.915808 \n",
"MAN1C1\\218918_at 6.583388 6.742747 \n",
"SGSM3\\214779_s_at 6.480099 6.975206 \n",
"LOC100508009\\231516_at 0.814985 1.810900 \n",
"ASCL3\\221161_at 1.251083 1.344811 \n",
"DALRD3\\221934_s_at 6.343070 6.658169 \n",
"DAPK2\\206324_s_at 6.336778 6.174706 \n",
"NUP155\\206550_s_at 5.763932 5.789187 \n",
"TMF1\\215855_s_at 6.901917 6.290164 \n",
"LOC100505584\\216336_x_at 8.082910 9.816838 \n",
"ARID1B\\1566990_x_at 7.043224 6.658440 \n",
"LOC100287105\\1570171_at 4.693548 4.466510 \n",
"UTRN\\225093_at 9.910094 9.638782 \n",
"HIST3H3\\208572_at 1.286769 1.156630 \n",
"ZNF316\\227170_at 5.000189 5.288632 \n",
"ETV6\\205585_at 5.425627 4.660284 \n",
"LOC400550\\243059_at 3.720858 5.915354 \n",
"B3GAT2\\234146_at 1.905255 1.575458 \n",
"HMGB4\\230473_s_at 2.196421 0.710649 \n",
"CMTM6\\217947_at 11.117546 10.326677 \n",
"BRAP\\209922_at 4.252575 5.015266 \n",
"BARD1\\205345_at 7.049707 6.193521 \n",
"MR1\\207565_s_at 5.230975 5.953328 \n",
"SORT1\\212797_at 5.082562 7.390246 \n",
"FLJ31485\\243351_at 5.677080 4.700828 \n",
"BPI\\205557_at 1.021863 4.347935 \n",
"CECR3\\1564352_at 4.007599 4.303079 \n",
"\n",
" GSE8581GSM212855 GSE8581GSM212070 \\\n",
"KIAA1377\\235956_at 4.924318 8.004900 \n",
"ZNF358\\226260_x_at 4.085595 4.767745 \n",
"GPR135\\214503_x_at 1.087890 1.194270 \n",
"GPATCH2\\242224_at 3.584397 5.486096 \n",
"RPL24\\214143_x_at 12.630738 12.627675 \n",
"PALM2\\1554640_at 6.681140 6.004290 \n",
"LOC339316\\242084_at 1.084091 1.457789 \n",
"FECH\\203115_at 4.090447 6.350764 \n",
"KCNJ9\\207527_at 2.253039 3.360196 \n",
"C21orf96\\220918_at 4.885101 5.563570 \n",
"SAT2\\225272_at 7.434945 8.948992 \n",
"EHD1\\209038_s_at 5.613700 6.709029 \n",
"CBLB\\208348_s_at 0.603587 2.026049 \n",
"C20orf85\\229542_at 3.488888 8.462748 \n",
"UGGT1\\218257_s_at 5.516945 6.552457 \n",
"LOC283585\\1561442_at 3.484486 3.133233 \n",
"EMP2\\204975_at 10.720920 12.007297 \n",
"LHFP\\218656_s_at 9.158880 10.142222 \n",
"SNCAIP\\237834_at 2.748893 1.926686 \n",
"RDH8\\220683_at 2.713984 4.919788 \n",
"SRSF4\\239512_at 7.413916 8.478094 \n",
"ACTB\\213867_x_at 13.328871 13.241964 \n",
"FAM182B\\215487_x_at 2.018987 4.134714 \n",
"C6orf108\\213871_s_at 1.206312 1.756195 \n",
"CSRNP2\\225042_s_at 6.343104 7.006074 \n",
"SLCO2B1\\203473_at 8.260534 9.819708 \n",
"MYNN\\237510_at 3.842748 4.088854 \n",
"NAP1L1\\208752_x_at 10.402511 10.936770 \n",
"ADAM28\\205997_at 3.875996 6.319249 \n",
"LOC100507248\\235236_at 2.399652 -1.327830 \n",
"PHF8\\238837_at 0.053806 2.333670 \n",
"C9orf96\\1554787_at 2.258263 1.780310 \n",
"TNPO2\\210585_s_at 3.838054 5.018616 \n",
"FLJ31485\\239569_at 3.630510 4.570056 \n",
"PUM1\\201164_s_at 8.274676 9.174604 \n",
"COX4I1\\202698_x_at 10.950461 11.406848 \n",
"IZUMO4\\215734_at 4.583639 4.245769 \n",
"TPSAB1\\216485_s_at 2.022698 2.780024 \n",
"LMAN1L\\220420_at 1.608904 1.616240 \n",
"LY6K\\223687_s_at 4.844717 4.438838 \n",
"ACAD10\\238655_at 4.244278 4.565335 \n",
"TIMM22\\219184_x_at 4.830484 6.513282 \n",
"HUS1\\217618_x_at 4.663669 5.843750 \n",
"EPHA7\\206852_at 3.774987 0.199914 \n",
"CSH1\\208069_x_at 0.164168 0.208342 \n",
"FMNL2\\242665_at 3.526682 5.483925 \n",
"PUS3\\221277_s_at 5.809250 7.054393 \n",
"CELF4\\231220_at -0.357444 3.528621 \n",
"RBM6\\228030_at 8.188223 9.498291 \n",
"AVIL\\233333_x_at 6.083077 7.272760 \n",
"... ... ... \n",
"MON1B\\233557_s_at 7.060609 8.283028 \n",
"CLLU1\\1558185_at 2.790488 3.794156 \n",
"KTN1\\214709_s_at 9.292545 10.518791 \n",
"KRTAP4-7\\216810_at 4.064762 2.740112 \n",
"RBKS\\219222_at 5.608419 6.695047 \n",
"LOC100506621\\227061_at 7.770505 8.117565 \n",
"CCDC67\\1554071_at 2.846279 1.156487 \n",
"MCM9\\219673_at 5.325278 6.556319 \n",
"LOC730101\\213248_at 4.264191 5.974096 \n",
"LOC100508546\\244037_at 1.383160 4.898866 \n",
"RNPS1\\200060_s_at 8.672252 10.146887 \n",
"C8orf74\\1569246_a_at 3.966809 4.746420 \n",
"UTP14C\\203614_at 7.330711 8.601734 \n",
"RHEB\\201452_at 4.723782 4.633396 \n",
"CXCL16\\223454_at 8.601964 9.486413 \n",
"PSPC1\\218371_s_at 6.230136 7.889607 \n",
"SIK3\\213034_at 7.978013 8.554777 \n",
"ACOT9\\221641_s_at 9.248853 9.179200 \n",
"KIAA1661\\215943_at 3.284806 4.135313 \n",
"STEAP2\\225871_at 8.131980 7.544254 \n",
"AKAP5\\207800_at 0.980252 0.912205 \n",
"C1orf57\\223272_s_at 6.514338 7.202809 \n",
"C7orf30\\226385_s_at 8.811998 9.851763 \n",
"BAX\\208478_s_at 4.501866 5.761283 \n",
"MAN1C1\\218918_at 6.217508 7.655159 \n",
"SGSM3\\214779_s_at 5.502980 7.249825 \n",
"LOC100508009\\231516_at 0.980647 0.710578 \n",
"ASCL3\\221161_at 1.827514 2.201690 \n",
"DALRD3\\221934_s_at 5.783467 8.331239 \n",
"DAPK2\\206324_s_at 5.848886 7.684854 \n",
"NUP155\\206550_s_at 5.309784 6.276657 \n",
"TMF1\\215855_s_at 5.627009 7.228078 \n",
"LOC100505584\\216336_x_at 11.912272 10.181450 \n",
"ARID1B\\1566990_x_at 3.971847 7.161868 \n",
"LOC100287105\\1570171_at 2.796884 0.496319 \n",
"UTRN\\225093_at 9.227060 10.398060 \n",
"HIST3H3\\208572_at -0.589066 2.876366 \n",
"ZNF316\\227170_at 3.610665 6.449428 \n",
"ETV6\\205585_at 4.686304 5.703884 \n",
"LOC400550\\243059_at 4.588151 6.245929 \n",
"B3GAT2\\234146_at 1.176240 1.627682 \n",
"HMGB4\\230473_s_at 3.439078 1.771387 \n",
"CMTM6\\217947_at 10.614084 11.129753 \n",
"BRAP\\209922_at 3.479696 5.331078 \n",
"BARD1\\205345_at 5.579328 7.003006 \n",
"MR1\\207565_s_at 5.426516 6.940167 \n",
"SORT1\\212797_at 5.628421 7.536076 \n",
"FLJ31485\\243351_at 4.613101 4.765312 \n",
"BPI\\205557_at 4.324141 3.819515 \n",
"CECR3\\1564352_at 2.497137 4.297177 \n",
"\n",
" GSE8581GSM212810 GSE8581GSM210193 \\\n",
"KIAA1377\\235956_at 2.411315 6.670685 \n",
"ZNF358\\226260_x_at -1.447194 4.025853 \n",
"GPR135\\214503_x_at -1.321647 0.938911 \n",
"GPATCH2\\242224_at -1.439762 5.385900 \n",
"RPL24\\214143_x_at -1.703159 12.229774 \n",
"PALM2\\1554640_at 2.274962 4.748209 \n",
"LOC339316\\242084_at 2.189900 -0.265294 \n",
"FECH\\203115_at -1.860861 5.720448 \n",
"KCNJ9\\207527_at -1.547046 4.613791 \n",
"C21orf96\\220918_at 2.084779 5.801756 \n",
"SAT2\\225272_at 1.320987 7.738741 \n",
"EHD1\\209038_s_at 0.626093 4.729270 \n",
"CBLB\\208348_s_at 0.551934 3.633629 \n",
"C20orf85\\229542_at 1.447971 6.153043 \n",
"UGGT1\\218257_s_at 1.104357 6.008482 \n",
"LOC283585\\1561442_at 0.538767 3.861102 \n",
"EMP2\\204975_at -1.408148 10.843474 \n",
"LHFP\\218656_s_at 0.891201 10.167130 \n",
"SNCAIP\\237834_at 2.686270 2.555478 \n",
"RDH8\\220683_at -0.327627 4.501879 \n",
"SRSF4\\239512_at 1.221227 7.565925 \n",
"ACTB\\213867_x_at 2.947561 12.791541 \n",
"FAM182B\\215487_x_at 2.393227 2.583846 \n",
"C6orf108\\213871_s_at 0.354204 2.465766 \n",
"CSRNP2\\225042_s_at -1.647974 6.100008 \n",
"SLCO2B1\\203473_at -1.396168 8.526370 \n",
"MYNN\\237510_at 1.132814 3.943378 \n",
"NAP1L1\\208752_x_at -2.209909 10.745221 \n",
"ADAM28\\205997_at -1.366403 4.995385 \n",
"LOC100507248\\235236_at 0.643810 2.481676 \n",
"PHF8\\238837_at -1.051005 0.881030 \n",
"C9orf96\\1554787_at 2.060843 3.286591 \n",
"TNPO2\\210585_s_at -0.675588 2.092505 \n",
"FLJ31485\\239569_at -0.911096 4.624698 \n",
"PUM1\\201164_s_at 1.454344 8.494348 \n",
"COX4I1\\202698_x_at -1.125409 10.633368 \n",
"IZUMO4\\215734_at -2.438604 2.911114 \n",
"TPSAB1\\216485_s_at 0.424202 0.800877 \n",
"LMAN1L\\220420_at 2.044873 1.861777 \n",
"LY6K\\223687_s_at 0.294900 3.856249 \n",
"ACAD10\\238655_at -0.332001 4.354438 \n",
"TIMM22\\219184_x_at 0.089715 6.105655 \n",
"HUS1\\217618_x_at 1.564685 6.010276 \n",
"EPHA7\\206852_at -1.506381 3.202302 \n",
"CSH1\\208069_x_at -0.527080 -0.023990 \n",
"FMNL2\\242665_at -1.352127 6.537523 \n",
"PUS3\\221277_s_at -1.097996 6.323484 \n",
"CELF4\\231220_at 0.402307 -0.135939 \n",
"RBM6\\228030_at 2.064152 9.045170 \n",
"AVIL\\233333_x_at 3.514526 6.478228 \n",
"... ... ... \n",
"MON1B\\233557_s_at 1.551398 6.111117 \n",
"CLLU1\\1558185_at 1.574295 3.283889 \n",
"KTN1\\214709_s_at 1.246262 10.112453 \n",
"KRTAP4-7\\216810_at 1.139371 2.688896 \n",
"RBKS\\219222_at 1.178052 4.758532 \n",
"LOC100506621\\227061_at 1.858896 8.021902 \n",
"CCDC67\\1554071_at -4.174082 -1.221717 \n",
"MCM9\\219673_at 1.405235 6.485189 \n",
"LOC730101\\213248_at -0.235853 5.628036 \n",
"LOC100508546\\244037_at -1.920762 4.565877 \n",
"RNPS1\\200060_s_at 0.158815 8.911913 \n",
"C8orf74\\1569246_a_at 1.012318 1.834861 \n",
"UTP14C\\203614_at -2.632674 8.122093 \n",
"RHEB\\201452_at -0.604369 2.497939 \n",
"CXCL16\\223454_at 0.336123 8.215048 \n",
"PSPC1\\218371_s_at -2.234112 7.393090 \n",
"SIK3\\213034_at 1.962497 7.728315 \n",
"ACOT9\\221641_s_at -0.759507 7.814621 \n",
"KIAA1661\\215943_at 1.865974 1.637773 \n",
"STEAP2\\225871_at -1.019691 6.642846 \n",
"AKAP5\\207800_at -2.130511 3.373133 \n",
"C1orf57\\223272_s_at -1.962480 6.704014 \n",
"C7orf30\\226385_s_at 1.506125 9.122683 \n",
"BAX\\208478_s_at 2.141668 6.202324 \n",
"MAN1C1\\218918_at 1.364606 6.778117 \n",
"SGSM3\\214779_s_at 0.897953 6.538965 \n",
"LOC100508009\\231516_at -0.739851 1.229330 \n",
"ASCL3\\221161_at -0.836759 0.725732 \n",
"DALRD3\\221934_s_at -0.712632 6.685029 \n",
"DAPK2\\206324_s_at 1.262565 6.172818 \n",
"NUP155\\206550_s_at -1.643888 5.657866 \n",
"TMF1\\215855_s_at 1.701886 6.290089 \n",
"LOC100505584\\216336_x_at -1.755205 8.662366 \n",
"ARID1B\\1566990_x_at -1.014234 6.987150 \n",
"LOC100287105\\1570171_at -2.507304 4.189840 \n",
"UTRN\\225093_at 1.566776 9.608661 \n",
"HIST3H3\\208572_at 1.766430 -0.396998 \n",
"ZNF316\\227170_at 2.224784 4.808720 \n",
"ETV6\\205585_at 1.654825 4.405141 \n",
"LOC400550\\243059_at -0.320133 5.678018 \n",
"B3GAT2\\234146_at 0.125400 1.377540 \n",
"HMGB4\\230473_s_at 1.225337 1.973435 \n",
"CMTM6\\217947_at -0.803652 9.888813 \n",
"BRAP\\209922_at 0.148296 4.329633 \n",
"BARD1\\205345_at -0.610828 5.801891 \n",
"MR1\\207565_s_at -2.418720 6.156089 \n",
"SORT1\\212797_at -0.055522 6.785197 \n",
"FLJ31485\\243351_at 3.323658 4.587989 \n",
"BPI\\205557_at 1.737929 4.419694 \n",
"CECR3\\1564352_at 0.328388 4.361979 \n",
"\n",
" ... GSE8581GSM210979 \\\n",
"KIAA1377\\235956_at ... 7.888354 \n",
"ZNF358\\226260_x_at ... 4.780016 \n",
"GPR135\\214503_x_at ... 0.686541 \n",
"GPATCH2\\242224_at ... 5.263271 \n",
"RPL24\\214143_x_at ... 12.501332 \n",
"PALM2\\1554640_at ... 5.663384 \n",
"LOC339316\\242084_at ... 1.123342 \n",
"FECH\\203115_at ... 6.834496 \n",
"KCNJ9\\207527_at ... 4.069548 \n",
"C21orf96\\220918_at ... 5.384008 \n",
"SAT2\\225272_at ... 7.510827 \n",
"EHD1\\209038_s_at ... 5.031285 \n",
"CBLB\\208348_s_at ... 4.673251 \n",
"C20orf85\\229542_at ... 6.658311 \n",
"UGGT1\\218257_s_at ... 6.032028 \n",
"LOC283585\\1561442_at ... 3.705093 \n",
"EMP2\\204975_at ... 11.797297 \n",
"LHFP\\218656_s_at ... 10.192170 \n",
"SNCAIP\\237834_at ... 3.470042 \n",
"RDH8\\220683_at ... 3.168956 \n",
"SRSF4\\239512_at ... 8.778008 \n",
"ACTB\\213867_x_at ... 12.878790 \n",
"FAM182B\\215487_x_at ... 2.849927 \n",
"C6orf108\\213871_s_at ... 2.053257 \n",
"CSRNP2\\225042_s_at ... 5.625344 \n",
"SLCO2B1\\203473_at ... 8.346997 \n",
"MYNN\\237510_at ... 4.780258 \n",
"NAP1L1\\208752_x_at ... 10.770474 \n",
"ADAM28\\205997_at ... 3.859880 \n",
"LOC100507248\\235236_at ... 0.497914 \n",
"PHF8\\238837_at ... 1.816514 \n",
"C9orf96\\1554787_at ... 1.401762 \n",
"TNPO2\\210585_s_at ... 1.812305 \n",
"FLJ31485\\239569_at ... 4.128005 \n",
"PUM1\\201164_s_at ... 9.462829 \n",
"COX4I1\\202698_x_at ... 10.422706 \n",
"IZUMO4\\215734_at ... 3.221716 \n",
"TPSAB1\\216485_s_at ... 0.322597 \n",
"LMAN1L\\220420_at ... 3.166168 \n",
"LY6K\\223687_s_at ... 4.182668 \n",
"ACAD10\\238655_at ... 4.449951 \n",
"TIMM22\\219184_x_at ... 6.771767 \n",
"HUS1\\217618_x_at ... 5.769928 \n",
"EPHA7\\206852_at ... 3.590913 \n",
"CSH1\\208069_x_at ... 0.494426 \n",
"FMNL2\\242665_at ... 6.091905 \n",
"PUS3\\221277_s_at ... 6.953766 \n",
"CELF4\\231220_at ... 0.166548 \n",
"RBM6\\228030_at ... 9.580609 \n",
"AVIL\\233333_x_at ... 7.190635 \n",
"... ... ... \n",
"MON1B\\233557_s_at ... 6.411186 \n",
"CLLU1\\1558185_at ... -0.200051 \n",
"KTN1\\214709_s_at ... 10.828573 \n",
"KRTAP4-7\\216810_at ... 3.299444 \n",
"RBKS\\219222_at ... 5.539295 \n",
"LOC100506621\\227061_at ... 6.946345 \n",
"CCDC67\\1554071_at ... 0.700120 \n",
"MCM9\\219673_at ... 6.156712 \n",
"LOC730101\\213248_at ... 6.084107 \n",
"LOC100508546\\244037_at ... 3.729879 \n",
"RNPS1\\200060_s_at ... 8.891999 \n",
"C8orf74\\1569246_a_at ... 4.522859 \n",
"UTP14C\\203614_at ... 8.575717 \n",
"RHEB\\201452_at ... 0.429171 \n",
"CXCL16\\223454_at ... 7.689760 \n",
"PSPC1\\218371_s_at ... 7.131188 \n",
"SIK3\\213034_at ... 8.131667 \n",
"ACOT9\\221641_s_at ... 7.840388 \n",
"KIAA1661\\215943_at ... 1.571546 \n",
"STEAP2\\225871_at ... 7.170436 \n",
"AKAP5\\207800_at ... 3.239957 \n",
"C1orf57\\223272_s_at ... 6.740887 \n",
"C7orf30\\226385_s_at ... 9.229444 \n",
"BAX\\208478_s_at ... 4.750446 \n",
"MAN1C1\\218918_at ... 6.401467 \n",
"SGSM3\\214779_s_at ... 5.941064 \n",
"LOC100508009\\231516_at ... 2.959913 \n",
"ASCL3\\221161_at ... 1.347926 \n",
"DALRD3\\221934_s_at ... 6.582208 \n",
"DAPK2\\206324_s_at ... 6.513636 \n",
"NUP155\\206550_s_at ... 5.756418 \n",
"TMF1\\215855_s_at ... 7.134426 \n",
"LOC100505584\\216336_x_at ... 8.983002 \n",
"ARID1B\\1566990_x_at ... 6.915891 \n",
"LOC100287105\\1570171_at ... 4.805323 \n",
"UTRN\\225093_at ... 10.277857 \n",
"HIST3H3\\208572_at ... 1.981359 \n",
"ZNF316\\227170_at ... 5.483455 \n",
"ETV6\\205585_at ... 4.634884 \n",
"LOC400550\\243059_at ... 3.835964 \n",
"B3GAT2\\234146_at ... 3.713476 \n",
"HMGB4\\230473_s_at ... 1.142165 \n",
"CMTM6\\217947_at ... 10.930656 \n",
"BRAP\\209922_at ... 4.418021 \n",
"BARD1\\205345_at ... 7.624445 \n",
"MR1\\207565_s_at ... 5.215585 \n",
"SORT1\\212797_at ... 5.026180 \n",
"FLJ31485\\243351_at ... 5.163277 \n",
"BPI\\205557_at ... 0.860836 \n",
"CECR3\\1564352_at ... 4.470934 \n",
"\n",
" GSE8581GSM213017 GSE8581GSM211007 \\\n",
"KIAA1377\\235956_at 6.538960 7.314416 \n",
"ZNF358\\226260_x_at 4.606946 5.232454 \n",
"GPR135\\214503_x_at 0.696047 1.137484 \n",
"GPATCH2\\242224_at 3.356482 5.831609 \n",
"RPL24\\214143_x_at 12.276255 12.471353 \n",
"PALM2\\1554640_at 5.626687 6.290896 \n",
"LOC339316\\242084_at 0.006305 4.473248 \n",
"FECH\\203115_at 5.207846 5.843306 \n",
"KCNJ9\\207527_at 3.205654 3.604522 \n",
"C21orf96\\220918_at 3.163640 5.905125 \n",
"SAT2\\225272_at 7.241602 7.443913 \n",
"EHD1\\209038_s_at 3.642690 2.643683 \n",
"CBLB\\208348_s_at 2.894183 1.403611 \n",
"C20orf85\\229542_at 6.841860 6.844750 \n",
"UGGT1\\218257_s_at 4.263155 5.904243 \n",
"LOC283585\\1561442_at 1.710636 4.286031 \n",
"EMP2\\204975_at 11.277770 11.592742 \n",
"LHFP\\218656_s_at 9.059190 9.559033 \n",
"SNCAIP\\237834_at -0.904038 4.527971 \n",
"RDH8\\220683_at 1.150722 5.495113 \n",
"SRSF4\\239512_at 6.416321 8.609762 \n",
"ACTB\\213867_x_at 13.138233 12.970985 \n",
"FAM182B\\215487_x_at 1.149526 3.348261 \n",
"C6orf108\\213871_s_at 2.421000 3.287985 \n",
"CSRNP2\\225042_s_at 5.452931 6.387033 \n",
"SLCO2B1\\203473_at 8.514296 9.381606 \n",
"MYNN\\237510_at 3.285414 3.572114 \n",
"NAP1L1\\208752_x_at 9.792940 10.982587 \n",
"ADAM28\\205997_at 5.675847 2.037948 \n",
"LOC100507248\\235236_at 2.766845 1.421420 \n",
"PHF8\\238837_at 0.384713 2.759429 \n",
"C9orf96\\1554787_at 3.062583 4.032815 \n",
"TNPO2\\210585_s_at 1.708638 2.571538 \n",
"FLJ31485\\239569_at 2.735113 5.520036 \n",
"PUM1\\201164_s_at 8.449215 9.270368 \n",
"COX4I1\\202698_x_at 10.628227 10.927074 \n",
"IZUMO4\\215734_at 3.966920 2.208118 \n",
"TPSAB1\\216485_s_at 0.241108 1.373153 \n",
"LMAN1L\\220420_at 0.785910 4.803460 \n",
"LY6K\\223687_s_at 1.804074 4.364804 \n",
"ACAD10\\238655_at 3.581809 5.354794 \n",
"TIMM22\\219184_x_at 5.784881 6.726572 \n",
"HUS1\\217618_x_at 5.373325 5.535664 \n",
"EPHA7\\206852_at 1.877579 1.158111 \n",
"CSH1\\208069_x_at 0.546393 1.646955 \n",
"FMNL2\\242665_at 4.495970 5.993219 \n",
"PUS3\\221277_s_at 5.959842 6.140368 \n",
"CELF4\\231220_at -0.291474 0.519119 \n",
"RBM6\\228030_at 9.308680 9.745452 \n",
"AVIL\\233333_x_at 5.107085 7.709208 \n",
"... ... ... \n",
"MON1B\\233557_s_at 6.440970 7.718211 \n",
"CLLU1\\1558185_at 3.760445 1.356854 \n",
"KTN1\\214709_s_at 9.403285 10.343597 \n",
"KRTAP4-7\\216810_at 2.225593 4.368468 \n",
"RBKS\\219222_at 5.411389 6.204941 \n",
"LOC100506621\\227061_at 7.382287 8.425191 \n",
"CCDC67\\1554071_at -0.228895 2.423452 \n",
"MCM9\\219673_at 5.207772 6.062892 \n",
"LOC730101\\213248_at 5.177093 5.802333 \n",
"LOC100508546\\244037_at 3.069190 2.968163 \n",
"RNPS1\\200060_s_at 7.953981 9.034595 \n",
"C8orf74\\1569246_a_at 4.420981 5.963370 \n",
"UTP14C\\203614_at 7.755288 8.397606 \n",
"RHEB\\201452_at 3.956540 1.644807 \n",
"CXCL16\\223454_at 8.066676 8.979814 \n",
"PSPC1\\218371_s_at 5.947082 7.035789 \n",
"SIK3\\213034_at 7.260054 7.847640 \n",
"ACOT9\\221641_s_at 7.504215 8.411443 \n",
"KIAA1661\\215943_at 0.154868 4.131713 \n",
"STEAP2\\225871_at 5.926773 6.827387 \n",
"AKAP5\\207800_at 1.053104 3.483132 \n",
"C1orf57\\223272_s_at 6.595195 6.685015 \n",
"C7orf30\\226385_s_at 8.423028 9.110016 \n",
"BAX\\208478_s_at 4.550014 5.028887 \n",
"MAN1C1\\218918_at 6.305770 6.768012 \n",
"SGSM3\\214779_s_at 5.356978 6.027309 \n",
"LOC100508009\\231516_at 0.891940 2.153809 \n",
"ASCL3\\221161_at 2.185626 3.873656 \n",
"DALRD3\\221934_s_at 5.760176 6.454429 \n",
"DAPK2\\206324_s_at 5.814207 6.558405 \n",
"NUP155\\206550_s_at 5.360438 5.776744 \n",
"TMF1\\215855_s_at 6.639760 7.250412 \n",
"LOC100505584\\216336_x_at 8.092414 9.432051 \n",
"ARID1B\\1566990_x_at 3.020854 7.189617 \n",
"LOC100287105\\1570171_at 3.401112 5.732815 \n",
"UTRN\\225093_at 9.241731 10.015582 \n",
"HIST3H3\\208572_at -0.848611 0.938083 \n",
"ZNF316\\227170_at 4.643371 5.596381 \n",
"ETV6\\205585_at 4.554270 5.222492 \n",
"LOC400550\\243059_at 4.854165 4.917408 \n",
"B3GAT2\\234146_at 2.656606 2.477006 \n",
"HMGB4\\230473_s_at 1.185105 4.201320 \n",
"CMTM6\\217947_at 10.071798 11.387102 \n",
"BRAP\\209922_at 0.507516 3.151500 \n",
"BARD1\\205345_at 5.735102 7.444344 \n",
"MR1\\207565_s_at 5.203107 6.598879 \n",
"SORT1\\212797_at 5.021151 6.463953 \n",
"FLJ31485\\243351_at 4.226216 5.596187 \n",
"BPI\\205557_at 3.239855 2.144037 \n",
"CECR3\\1564352_at 4.405128 2.572625 \n",
"\n",
" GSE8581GSM210192 GSE8581GSM213020 \\\n",
"KIAA1377\\235956_at 5.892823 6.554481 \n",
"ZNF358\\226260_x_at 4.568361 4.537433 \n",
"GPR135\\214503_x_at 0.213963 0.964066 \n",
"GPATCH2\\242224_at 4.992265 5.039222 \n",
"RPL24\\214143_x_at 12.024201 12.642733 \n",
"PALM2\\1554640_at 4.591548 5.503263 \n",
"LOC339316\\242084_at -0.392482 0.871686 \n",
"FECH\\203115_at 5.312484 4.892386 \n",
"KCNJ9\\207527_at 2.567180 3.076275 \n",
"C21orf96\\220918_at 4.462373 5.391685 \n",
"SAT2\\225272_at 8.204175 7.967803 \n",
"EHD1\\209038_s_at 4.169444 5.328567 \n",
"CBLB\\208348_s_at 2.498493 0.506145 \n",
"C20orf85\\229542_at 5.872060 7.208459 \n",
"UGGT1\\218257_s_at 5.303737 5.705884 \n",
"LOC283585\\1561442_at 2.594986 4.520120 \n",
"EMP2\\204975_at 10.794018 11.989767 \n",
"LHFP\\218656_s_at 9.442676 9.684657 \n",
"SNCAIP\\237834_at 3.324350 3.490403 \n",
"RDH8\\220683_at 4.482984 4.278468 \n",
"SRSF4\\239512_at 7.581886 8.321924 \n",
"ACTB\\213867_x_at 12.558581 13.419697 \n",
"FAM182B\\215487_x_at 1.850631 0.647139 \n",
"C6orf108\\213871_s_at 4.210568 2.441361 \n",
"CSRNP2\\225042_s_at 6.038015 6.148487 \n",
"SLCO2B1\\203473_at 9.238491 9.320160 \n",
"MYNN\\237510_at 4.307807 3.838034 \n",
"NAP1L1\\208752_x_at 10.398231 11.065046 \n",
"ADAM28\\205997_at 5.234149 6.298711 \n",
"LOC100507248\\235236_at 0.274554 2.516663 \n",
"PHF8\\238837_at 0.919752 0.762944 \n",
"C9orf96\\1554787_at 2.085414 3.011116 \n",
"TNPO2\\210585_s_at 4.306955 3.045516 \n",
"FLJ31485\\239569_at 4.637552 4.818927 \n",
"PUM1\\201164_s_at 8.673532 9.521914 \n",
"COX4I1\\202698_x_at 10.536451 11.284066 \n",
"IZUMO4\\215734_at 4.387459 3.835853 \n",
"TPSAB1\\216485_s_at 0.022361 0.703632 \n",
"LMAN1L\\220420_at 1.394646 2.410542 \n",
"LY6K\\223687_s_at 2.702303 1.110316 \n",
"ACAD10\\238655_at 4.535288 4.514318 \n",
"TIMM22\\219184_x_at 5.751314 6.477974 \n",
"HUS1\\217618_x_at 5.604062 5.633858 \n",
"EPHA7\\206852_at 0.885106 2.495519 \n",
"CSH1\\208069_x_at 0.601506 3.274652 \n",
"FMNL2\\242665_at 6.431006 4.795767 \n",
"PUS3\\221277_s_at 6.310242 6.235164 \n",
"CELF4\\231220_at 2.435509 0.474109 \n",
"RBM6\\228030_at 8.250696 9.392914 \n",
"AVIL\\233333_x_at 6.657111 6.573403 \n",
"... ... ... \n",
"MON1B\\233557_s_at 6.492505 7.361803 \n",
"CLLU1\\1558185_at -0.964424 0.124328 \n",
"KTN1\\214709_s_at 9.697475 10.437482 \n",
"KRTAP4-7\\216810_at 1.189622 4.000316 \n",
"RBKS\\219222_at 4.763821 5.966758 \n",
"LOC100506621\\227061_at 6.190012 7.384905 \n",
"CCDC67\\1554071_at 0.243413 3.231492 \n",
"MCM9\\219673_at 6.130558 6.280587 \n",
"LOC730101\\213248_at 5.042351 5.277966 \n",
"LOC100508546\\244037_at 4.364895 1.032228 \n",
"RNPS1\\200060_s_at 9.062535 9.309429 \n",
"C8orf74\\1569246_a_at 4.814381 3.303941 \n",
"UTP14C\\203614_at 8.035178 8.590939 \n",
"RHEB\\201452_at 4.890461 4.466386 \n",
"CXCL16\\223454_at 8.720945 8.943913 \n",
"PSPC1\\218371_s_at 7.294244 7.477669 \n",
"SIK3\\213034_at 7.622147 8.259889 \n",
"ACOT9\\221641_s_at 7.790433 8.638139 \n",
"KIAA1661\\215943_at 0.860454 0.499435 \n",
"STEAP2\\225871_at 6.316084 6.746796 \n",
"AKAP5\\207800_at 3.388520 1.650944 \n",
"C1orf57\\223272_s_at 7.120300 7.355307 \n",
"C7orf30\\226385_s_at 9.052321 9.141443 \n",
"BAX\\208478_s_at 6.286889 5.575055 \n",
"MAN1C1\\218918_at 6.937238 7.399257 \n",
"SGSM3\\214779_s_at 6.476560 5.856627 \n",
"LOC100508009\\231516_at 1.315792 0.238775 \n",
"ASCL3\\221161_at 2.863080 1.878725 \n",
"DALRD3\\221934_s_at 6.624623 6.385816 \n",
"DAPK2\\206324_s_at 6.266966 6.625050 \n",
"NUP155\\206550_s_at 5.280626 5.654484 \n",
"TMF1\\215855_s_at 6.137225 7.059755 \n",
"LOC100505584\\216336_x_at 8.614206 10.255855 \n",
"ARID1B\\1566990_x_at 6.719129 5.611276 \n",
"LOC100287105\\1570171_at 4.001865 3.472046 \n",
"UTRN\\225093_at 9.443418 10.313541 \n",
"HIST3H3\\208572_at 2.529259 0.210688 \n",
"ZNF316\\227170_at 5.228653 5.093509 \n",
"ETV6\\205585_at 5.008505 4.727093 \n",
"LOC400550\\243059_at 6.209835 6.165832 \n",
"B3GAT2\\234146_at 1.141858 0.080180 \n",
"HMGB4\\230473_s_at 3.796577 3.935149 \n",
"CMTM6\\217947_at 10.178316 11.016843 \n",
"BRAP\\209922_at 4.509461 4.517975 \n",
"BARD1\\205345_at 5.718608 6.613499 \n",
"MR1\\207565_s_at 6.072202 6.262719 \n",
"SORT1\\212797_at 6.556249 7.355034 \n",
"FLJ31485\\243351_at 4.388465 3.612706 \n",
"BPI\\205557_at 0.549590 3.909869 \n",
"CECR3\\1564352_at 3.996723 4.119672 \n",
"\n",
" GSE8581GSM210994 GSE8581GSM210010 \\\n",
"KIAA1377\\235956_at 7.427330 5.623677 \n",
"ZNF358\\226260_x_at 3.196739 3.986893 \n",
"GPR135\\214503_x_at -0.252259 0.214336 \n",
"GPATCH2\\242224_at 5.572077 4.678433 \n",
"RPL24\\214143_x_at 12.585993 12.109086 \n",
"PALM2\\1554640_at 5.310369 4.924789 \n",
"LOC339316\\242084_at 1.391069 -0.194356 \n",
"FECH\\203115_at 5.718230 5.333832 \n",
"KCNJ9\\207527_at 3.840896 3.597162 \n",
"C21orf96\\220918_at 4.537215 5.284943 \n",
"SAT2\\225272_at 7.214970 8.177086 \n",
"EHD1\\209038_s_at 1.194219 3.985938 \n",
"CBLB\\208348_s_at 1.890999 0.135535 \n",
"C20orf85\\229542_at 6.531349 3.587077 \n",
"UGGT1\\218257_s_at 5.735067 5.761126 \n",
"LOC283585\\1561442_at 4.288447 3.505434 \n",
"EMP2\\204975_at 11.484546 10.659693 \n",
"LHFP\\218656_s_at 9.931885 9.438902 \n",
"SNCAIP\\237834_at 0.654142 2.098797 \n",
"RDH8\\220683_at 5.238550 2.795484 \n",
"SRSF4\\239512_at 8.600660 7.747475 \n",
"ACTB\\213867_x_at 12.610037 12.449582 \n",
"FAM182B\\215487_x_at 3.622649 4.407672 \n",
"C6orf108\\213871_s_at 2.207599 2.172868 \n",
"CSRNP2\\225042_s_at 5.680344 5.882540 \n",
"SLCO2B1\\203473_at 8.343523 8.400751 \n",
"MYNN\\237510_at 3.913416 2.329247 \n",
"NAP1L1\\208752_x_at 10.883163 10.169750 \n",
"ADAM28\\205997_at 5.129015 4.205901 \n",
"LOC100507248\\235236_at 3.578105 2.022162 \n",
"PHF8\\238837_at 1.900142 -0.200908 \n",
"C9orf96\\1554787_at 1.542263 2.884143 \n",
"TNPO2\\210585_s_at 1.792347 2.022006 \n",
"FLJ31485\\239569_at 3.922987 4.594638 \n",
"PUM1\\201164_s_at 9.425923 8.175694 \n",
"COX4I1\\202698_x_at 10.729723 10.442591 \n",
"IZUMO4\\215734_at 3.551934 3.564061 \n",
"TPSAB1\\216485_s_at 1.926417 0.645914 \n",
"LMAN1L\\220420_at 2.427598 2.189227 \n",
"LY6K\\223687_s_at 4.526626 4.010046 \n",
"ACAD10\\238655_at 5.121140 3.469222 \n",
"TIMM22\\219184_x_at 5.982384 4.779969 \n",
"HUS1\\217618_x_at 6.031278 5.453458 \n",
"EPHA7\\206852_at 0.404598 3.397789 \n",
"CSH1\\208069_x_at 0.575980 2.113977 \n",
"FMNL2\\242665_at 6.155328 7.011809 \n",
"PUS3\\221277_s_at 6.703793 6.611894 \n",
"CELF4\\231220_at 3.179498 2.003573 \n",
"RBM6\\228030_at 10.222855 7.912560 \n",
"AVIL\\233333_x_at 6.356035 6.471448 \n",
"... ... ... \n",
"MON1B\\233557_s_at 6.280071 6.643899 \n",
"CLLU1\\1558185_at 0.007009 3.227231 \n",
"KTN1\\214709_s_at 10.219253 9.777232 \n",
"KRTAP4-7\\216810_at 2.156096 2.231165 \n",
"RBKS\\219222_at 5.916391 4.946553 \n",
"LOC100506621\\227061_at 7.763080 7.322523 \n",
"CCDC67\\1554071_at 0.267464 2.338519 \n",
"MCM9\\219673_at 5.896870 6.141386 \n",
"LOC730101\\213248_at 6.093664 5.559908 \n",
"LOC100508546\\244037_at 3.603454 2.715448 \n",
"RNPS1\\200060_s_at 8.807416 8.851462 \n",
"C8orf74\\1569246_a_at 4.218324 4.396194 \n",
"UTP14C\\203614_at 8.551051 7.873912 \n",
"RHEB\\201452_at 4.500146 2.375757 \n",
"CXCL16\\223454_at 8.278789 8.592207 \n",
"PSPC1\\218371_s_at 6.826167 6.530594 \n",
"SIK3\\213034_at 7.620117 7.406698 \n",
"ACOT9\\221641_s_at 8.072674 7.603500 \n",
"KIAA1661\\215943_at 4.370729 2.558929 \n",
"STEAP2\\225871_at 7.101986 6.221703 \n",
"AKAP5\\207800_at 0.955037 0.808261 \n",
"C1orf57\\223272_s_at 6.374612 6.479274 \n",
"C7orf30\\226385_s_at 9.071116 8.933115 \n",
"BAX\\208478_s_at 5.071591 5.964729 \n",
"MAN1C1\\218918_at 6.863133 6.620010 \n",
"SGSM3\\214779_s_at 6.019471 6.557572 \n",
"LOC100508009\\231516_at 2.161891 -0.271548 \n",
"ASCL3\\221161_at 3.481389 1.936025 \n",
"DALRD3\\221934_s_at 6.535386 5.936365 \n",
"DAPK2\\206324_s_at 5.898878 6.420723 \n",
"NUP155\\206550_s_at 5.879899 5.116348 \n",
"TMF1\\215855_s_at 6.960465 6.188907 \n",
"LOC100505584\\216336_x_at 9.316582 9.096483 \n",
"ARID1B\\1566990_x_at 6.995089 6.711302 \n",
"LOC100287105\\1570171_at 3.889658 3.857832 \n",
"UTRN\\225093_at 9.934789 9.209356 \n",
"HIST3H3\\208572_at 4.452576 2.046432 \n",
"ZNF316\\227170_at 4.529546 4.899219 \n",
"ETV6\\205585_at 4.823994 5.700418 \n",
"LOC400550\\243059_at 5.456901 4.670619 \n",
"B3GAT2\\234146_at 3.536140 0.672525 \n",
"HMGB4\\230473_s_at 2.021405 3.901861 \n",
"CMTM6\\217947_at 10.761393 10.173565 \n",
"BRAP\\209922_at 4.317355 3.179204 \n",
"BARD1\\205345_at 6.629858 5.432485 \n",
"MR1\\207565_s_at 6.137137 6.315622 \n",
"SORT1\\212797_at 6.665094 5.903407 \n",
"FLJ31485\\243351_at 4.759539 4.475967 \n",
"BPI\\205557_at 2.452711 2.145231 \n",
"CECR3\\1564352_at 4.514905 4.044753 \n",
"\n",
" GSE8581GSM210011 GSE8581GSM210007 GSE8581GSM213019 \n",
"KIAA1377\\235956_at 5.559804 6.104142 6.969680 \n",
"ZNF358\\226260_x_at 4.851469 3.962614 5.654816 \n",
"GPR135\\214503_x_at 0.566046 0.067900 -0.266347 \n",
"GPATCH2\\242224_at 4.641962 4.997518 5.041904 \n",
"RPL24\\214143_x_at 11.953891 11.624786 13.002877 \n",
"PALM2\\1554640_at 5.146977 5.019933 5.911052 \n",
"LOC339316\\242084_at 0.083697 3.514753 1.218781 \n",
"FECH\\203115_at 4.882795 5.789813 6.214107 \n",
"KCNJ9\\207527_at 1.285207 1.642979 4.039182 \n",
"C21orf96\\220918_at 4.878632 4.544145 6.354914 \n",
"SAT2\\225272_at 7.745654 7.629014 8.572253 \n",
"EHD1\\209038_s_at 4.281810 4.666552 5.242256 \n",
"CBLB\\208348_s_at 2.395208 3.197502 0.186754 \n",
"C20orf85\\229542_at 6.786636 6.914182 5.792871 \n",
"UGGT1\\218257_s_at 5.646946 5.580655 5.697907 \n",
"LOC283585\\1561442_at 4.012971 3.750939 4.374720 \n",
"EMP2\\204975_at 10.273108 10.974938 11.568312 \n",
"LHFP\\218656_s_at 8.614493 9.072494 9.847826 \n",
"SNCAIP\\237834_at 1.903358 3.349436 1.955607 \n",
"RDH8\\220683_at 2.430928 4.177711 4.846423 \n",
"SRSF4\\239512_at 7.589434 8.392601 8.622656 \n",
"ACTB\\213867_x_at 12.679300 12.432845 13.330623 \n",
"FAM182B\\215487_x_at 3.408984 3.727267 1.797312 \n",
"C6orf108\\213871_s_at 2.086094 1.788022 2.095864 \n",
"CSRNP2\\225042_s_at 5.875183 6.261409 6.810057 \n",
"SLCO2B1\\203473_at 9.045113 8.889014 9.842943 \n",
"MYNN\\237510_at 3.460952 3.317411 4.770649 \n",
"NAP1L1\\208752_x_at 10.456498 9.969458 11.191152 \n",
"ADAM28\\205997_at 5.297874 3.993122 5.034577 \n",
"LOC100507248\\235236_at 2.553985 -0.141042 3.280830 \n",
"PHF8\\238837_at 0.260471 0.137333 1.619676 \n",
"C9orf96\\1554787_at 3.452595 3.633559 0.805144 \n",
"TNPO2\\210585_s_at 2.772952 3.268816 3.725119 \n",
"FLJ31485\\239569_at 4.220338 4.644427 4.110689 \n",
"PUM1\\201164_s_at 8.123552 8.278528 9.520827 \n",
"COX4I1\\202698_x_at 10.516931 10.675004 11.483045 \n",
"IZUMO4\\215734_at 5.134899 3.869950 4.971139 \n",
"TPSAB1\\216485_s_at 1.024490 -0.121292 1.646753 \n",
"LMAN1L\\220420_at 2.269497 1.488505 2.667940 \n",
"LY6K\\223687_s_at 2.707023 3.570839 3.322880 \n",
"ACAD10\\238655_at 3.874984 4.280593 4.871326 \n",
"TIMM22\\219184_x_at 5.288362 5.545894 6.244668 \n",
"HUS1\\217618_x_at 5.839237 5.774929 5.465534 \n",
"EPHA7\\206852_at -0.173467 2.728247 3.904648 \n",
"CSH1\\208069_x_at 0.268351 0.506419 1.501908 \n",
"FMNL2\\242665_at 5.865367 6.039472 5.152058 \n",
"PUS3\\221277_s_at 6.316678 5.945692 7.125858 \n",
"CELF4\\231220_at 0.316586 -0.800551 -0.160679 \n",
"RBM6\\228030_at 7.941529 8.808716 9.672188 \n",
"AVIL\\233333_x_at 6.134972 6.028686 7.222264 \n",
"... ... ... ... \n",
"MON1B\\233557_s_at 7.154373 6.405061 6.969646 \n",
"CLLU1\\1558185_at 0.525067 2.545576 0.386038 \n",
"KTN1\\214709_s_at 9.765666 9.429413 10.550237 \n",
"KRTAP4-7\\216810_at 3.906371 2.807456 1.700799 \n",
"RBKS\\219222_at 5.777888 4.430118 6.200583 \n",
"LOC100506621\\227061_at 6.880881 7.502840 8.017187 \n",
"CCDC67\\1554071_at 2.860540 0.016924 -0.710642 \n",
"MCM9\\219673_at 5.830752 6.055306 6.385132 \n",
"LOC730101\\213248_at 4.932529 4.992519 6.580990 \n",
"LOC100508546\\244037_at 1.065910 3.543595 4.800848 \n",
"RNPS1\\200060_s_at 8.927802 8.675572 9.464456 \n",
"C8orf74\\1569246_a_at 1.711301 4.925235 1.969815 \n",
"UTP14C\\203614_at 7.310994 7.716230 8.639301 \n",
"RHEB\\201452_at 4.207651 3.423995 4.421594 \n",
"CXCL16\\223454_at 8.964350 8.768965 9.031031 \n",
"PSPC1\\218371_s_at 6.498798 6.342836 7.471773 \n",
"SIK3\\213034_at 7.638400 7.422620 8.434107 \n",
"ACOT9\\221641_s_at 8.391544 8.262889 8.341719 \n",
"KIAA1661\\215943_at -0.026417 0.001269 3.834772 \n",
"STEAP2\\225871_at 7.338317 5.990190 7.061323 \n",
"AKAP5\\207800_at 2.180963 1.017908 3.116330 \n",
"C1orf57\\223272_s_at 4.271597 6.080555 7.493967 \n",
"C7orf30\\226385_s_at 8.766519 8.582187 9.743210 \n",
"BAX\\208478_s_at 6.437599 5.580124 5.227425 \n",
"MAN1C1\\218918_at 6.248286 6.748421 7.307337 \n",
"SGSM3\\214779_s_at 6.265962 6.514209 6.515731 \n",
"LOC100508009\\231516_at 3.107577 1.807009 1.288778 \n",
"ASCL3\\221161_at 1.229871 2.364402 4.689098 \n",
"DALRD3\\221934_s_at 6.064210 6.503974 7.208312 \n",
"DAPK2\\206324_s_at 5.547712 6.288178 6.460918 \n",
"NUP155\\206550_s_at 5.056328 5.814168 5.992225 \n",
"TMF1\\215855_s_at 5.935240 6.379973 7.085053 \n",
"LOC100505584\\216336_x_at 10.313688 9.599377 9.511547 \n",
"ARID1B\\1566990_x_at 6.026610 6.801663 6.861558 \n",
"LOC100287105\\1570171_at 4.390365 4.126296 4.692935 \n",
"UTRN\\225093_at 9.069648 9.137393 10.477890 \n",
"HIST3H3\\208572_at -0.111016 0.831756 0.302477 \n",
"ZNF316\\227170_at 5.149950 4.447850 5.308212 \n",
"ETV6\\205585_at 4.969933 5.274616 4.586272 \n",
"LOC400550\\243059_at 4.239658 5.598508 5.056883 \n",
"B3GAT2\\234146_at 0.800894 1.226626 -0.418888 \n",
"HMGB4\\230473_s_at 0.221753 1.330432 2.412188 \n",
"CMTM6\\217947_at 10.378219 10.059845 11.053553 \n",
"BRAP\\209922_at 4.385003 4.397837 5.448458 \n",
"BARD1\\205345_at 5.495951 5.855873 7.085850 \n",
"MR1\\207565_s_at 6.195515 6.094489 5.978122 \n",
"SORT1\\212797_at 6.181027 6.315383 6.688852 \n",
"FLJ31485\\243351_at 4.051703 4.583555 4.557226 \n",
"BPI\\205557_at 5.314164 1.435842 4.217409 \n",
"CECR3\\1564352_at 3.865632 3.683932 3.858588 \n",
"\n",
"[42449 rows x 55 columns]"
]
},
"execution_count": 43,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from pandas import DataFrame\n",
"\n",
"hd_df = DataFrame(rows, columns = col_names, index = row_names)\n",
"hd_df"
]
},
{
"cell_type": "code",
"execution_count": 48,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"image/png": 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N+qalnfodiyoyun0ZUcp/rcNaxvYZOmH6khXbd+47dPLi7YdFkkDJ27tocGzb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\nQmCC\n"
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"%%R -i hd_df\n",
"\n",
"plot(density(hd_df[,1]))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Using the **control** and **treatment** sets made a few cells above, we build the \"design\" data frame showing which subjects are part of which set."
]
},
{
"cell_type": "code",
"execution_count": 49,
"metadata": {
"collapsed": false,
"scrolled": true
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>control</th>\n",
" <th>treatment</th>\n",
" </tr>\n",
" <tr>\n",
" <th>subject.inTrialId</th>\n",
" <th></th>\n",
" <th></th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>GSE8581GSM213034</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212811</th>\n",
" <td>True</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM213036</th>\n",
" <td>True</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212075</th>\n",
" <td>False</td>\n",
" <td>True</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM211008</th>\n",
" <td>True</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210090</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212855</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212070</th>\n",
" <td>True</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212810</th>\n",
" <td>False</td>\n",
" <td>True</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210193</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210071</th>\n",
" <td>False</td>\n",
" <td>True</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212069</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212849</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212787</th>\n",
" <td>True</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210015</th>\n",
" <td>True</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212853</th>\n",
" <td>True</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212790</th>\n",
" <td>True</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212067</th>\n",
" <td>True</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM211865</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210196</th>\n",
" <td>True</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212809</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210992</th>\n",
" <td>False</td>\n",
" <td>True</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM211009</th>\n",
" <td>False</td>\n",
" <td>True</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210014</th>\n",
" <td>True</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM213018</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212789</th>\n",
" <td>True</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210978</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM213037</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212074</th>\n",
" <td>False</td>\n",
" <td>True</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210993</th>\n",
" <td>False</td>\n",
" <td>True</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210087</th>\n",
" <td>True</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212068</th>\n",
" <td>True</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210012</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212854</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212852</th>\n",
" <td>False</td>\n",
" <td>True</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212848</th>\n",
" <td>False</td>\n",
" <td>True</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM211010</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM213035</th>\n",
" <td>True</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210194</th>\n",
" <td>False</td>\n",
" <td>True</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210008</th>\n",
" <td>False</td>\n",
" <td>True</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212788</th>\n",
" <td>False</td>\n",
" <td>True</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM211872</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM212850</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210188</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210009</th>\n",
" <td>True</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210979</th>\n",
" <td>True</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM213017</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM211007</th>\n",
" <td>False</td>\n",
" <td>True</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210192</th>\n",
" <td>True</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM213020</th>\n",
" <td>False</td>\n",
" <td>True</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210994</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210010</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210011</th>\n",
" <td>False</td>\n",
" <td>True</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM210007</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GSE8581GSM213019</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" control treatment\n",
"subject.inTrialId \n",
"GSE8581GSM213034 False False\n",
"GSE8581GSM212811 True False\n",
"GSE8581GSM213036 True False\n",
"GSE8581GSM212075 False True\n",
"GSE8581GSM211008 True False\n",
"GSE8581GSM210090 False False\n",
"GSE8581GSM212855 False False\n",
"GSE8581GSM212070 True False\n",
"GSE8581GSM212810 False True\n",
"GSE8581GSM210193 False False\n",
"GSE8581GSM210071 False True\n",
"GSE8581GSM212069 False False\n",
"GSE8581GSM212849 False False\n",
"GSE8581GSM212787 True False\n",
"GSE8581GSM210015 True False\n",
"GSE8581GSM212853 True False\n",
"GSE8581GSM212790 True False\n",
"GSE8581GSM212067 True False\n",
"GSE8581GSM211865 False False\n",
"GSE8581GSM210196 True False\n",
"GSE8581GSM212809 False False\n",
"GSE8581GSM210992 False True\n",
"GSE8581GSM211009 False True\n",
"GSE8581GSM210014 True False\n",
"GSE8581GSM213018 False False\n",
"GSE8581GSM212789 True False\n",
"GSE8581GSM210978 False False\n",
"GSE8581GSM213037 False False\n",
"GSE8581GSM212074 False True\n",
"GSE8581GSM210993 False True\n",
"GSE8581GSM210087 True False\n",
"GSE8581GSM212068 True False\n",
"GSE8581GSM210012 False False\n",
"GSE8581GSM212854 False False\n",
"GSE8581GSM212852 False True\n",
"GSE8581GSM212848 False True\n",
"GSE8581GSM211010 False False\n",
"GSE8581GSM213035 True False\n",
"GSE8581GSM210194 False True\n",
"GSE8581GSM210008 False True\n",
"GSE8581GSM212788 False True\n",
"GSE8581GSM211872 False False\n",
"GSE8581GSM212850 False False\n",
"GSE8581GSM210188 False False\n",
"GSE8581GSM210009 True False\n",
"GSE8581GSM210979 True False\n",
"GSE8581GSM213017 False False\n",
"GSE8581GSM211007 False True\n",
"GSE8581GSM210192 True False\n",
"GSE8581GSM213020 False True\n",
"GSE8581GSM210994 False False\n",
"GSE8581GSM210010 False False\n",
"GSE8581GSM210011 False True\n",
"GSE8581GSM210007 False False\n",
"GSE8581GSM213019 False False"
]
},
"execution_count": 49,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"design_df = DataFrame({'control': control[col_names], 'treatment': treatment[col_names]})\n",
"design_df"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Calling R differential analysis code (aka Advanced Analysis>'Marker Selection' in tranSMART)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Here we pass the data frames, initialized above in Python, to R. Jupyter will convert this to R. Handy feature!! Now we can also reuse all the nice R libraries which are not (yet) in Python."
]
},
{
"cell_type": "code",
"execution_count": 50,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"The rpy2.ipython extension is already loaded. To reload it, use:\n",
" %reload_ext rpy2.ipython\n"
]
}
],
"source": [
"%load_ext rpy2.ipython"
]
},
{
"cell_type": "code",
"execution_count": 51,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
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d5QYoDQWgNMBpFDjQfU3FzvXSBZSEUY4eRgFp/XyxCc0PiQ91XDYOtQgcGXVF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\nX4HnzqT5s2Q8FMlShgUiPxpFCKNGHVuLTdNArOf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},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"%%R -i hd_df -i design_df -o top_fit\n",
"\n",
"library(limma)\n",
"\n",
"design.matrix <- sapply(design_df, as.numeric)\n",
"contrast.matrix <- makeContrasts(control - treatment, levels = design.matrix)\n",
"\n",
"fit <- lmFit(hd_df, design.matrix)\n",
"fit <- contrasts.fit(fit, contrast.matrix)\n",
"fit <- eBayes(fit)\n",
"\n",
"contr=1\n",
"log_fc = fit$coefficients[, contr]/log(2)\n",
"p_value = -log10(fit$p.value[, contr])\n",
"plot(log_fc, p_value, ylab=\"-log10 p-value\", xlab=\"log2 fold change\")\n",
"\n",
"# alternative plots log fc x log odds: \n",
"#volcanoplot(fit)\n",
"\n",
"# \"send\" data back to Python: make a dataframe containing the important data and store \n",
"# in top_fit (the \"-o\" variable above) so that it can be accessed in python code \n",
"# in the subsequent code cells of this notebook (see flag '-o top_fit' above):\n",
"top_fit = data.frame(\n",
" probe = rownames(fit$coefficients),\n",
" log_fc = fit$coefficients[, contr],\n",
" t = fit$t[, contr],\n",
" p_value = fit$p.value[, contr],\n",
" b = fit$lods[, contr],\n",
" stringsAsFactors = FALSE\n",
")"
]
},
{
"cell_type": "code",
"execution_count": 52,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>probe</th>\n",
" <th>log_fc</th>\n",
" <th>t</th>\n",
" <th>p_value</th>\n",
" <th>b</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>KIAA1377\\235956_at</td>\n",
" <td>0.879185</td>\n",
" <td>0.576089</td>\n",
" <td>0.566838</td>\n",
" <td>-4.598590</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>ZNF358\\226260_x_at</td>\n",
" <td>0.516999</td>\n",
" <td>0.481906</td>\n",
" <td>0.631730</td>\n",
" <td>-4.599110</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>GPR135\\214503_x_at</td>\n",
" <td>-0.037486</td>\n",
" <td>-0.105517</td>\n",
" <td>0.916339</td>\n",
" <td>-4.600272</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>GPATCH2\\242224_at</td>\n",
" <td>0.245595</td>\n",
" <td>0.215820</td>\n",
" <td>0.829904</td>\n",
" <td>-4.600085</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>RPL24\\214143_x_at</td>\n",
" <td>1.012177</td>\n",
" <td>0.364221</td>\n",
" <td>0.717050</td>\n",
" <td>-4.599632</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>PALM2\\1554640_at</td>\n",
" <td>0.198167</td>\n",
" <td>0.165797</td>\n",
" <td>0.868907</td>\n",
" <td>-4.600186</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>LOC339316\\242084_at</td>\n",
" <td>0.001682</td>\n",
" <td>0.003089</td>\n",
" <td>0.997546</td>\n",
" <td>-4.600330</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>FECH\\203115_at</td>\n",
" <td>0.895703</td>\n",
" <td>0.707561</td>\n",
" <td>0.482120</td>\n",
" <td>-4.597713</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>KCNJ9\\207527_at</td>\n",
" <td>0.148250</td>\n",
" <td>0.182965</td>\n",
" <td>0.855479</td>\n",
" <td>-4.600154</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>C21orf96\\220918_at</td>\n",
" <td>0.286274</td>\n",
" <td>0.241679</td>\n",
" <td>0.809902</td>\n",
" <td>-4.600023</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>SAT2\\225272_at</td>\n",
" <td>0.785265</td>\n",
" <td>0.435954</td>\n",
" <td>0.664528</td>\n",
" <td>-4.599331</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>EHD1\\209038_s_at</td>\n",
" <td>0.858592</td>\n",
" <td>0.767820</td>\n",
" <td>0.445785</td>\n",
" <td>-4.597252</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>CBLB\\208348_s_at</td>\n",
" <td>0.376908</td>\n",
" <td>0.575643</td>\n",
" <td>0.567137</td>\n",
" <td>-4.598593</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>C20orf85\\229542_at</td>\n",
" <td>1.120739</td>\n",
" <td>0.718556</td>\n",
" <td>0.475370</td>\n",
" <td>-4.597631</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
" <td>UGGT1\\218257_s_at</td>\n",
" <td>0.220018</td>\n",
" <td>0.175489</td>\n",
" <td>0.861321</td>\n",
" <td>-4.600168</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>LOC283585\\1561442_at</td>\n",
" <td>-0.028199</td>\n",
" <td>-0.033870</td>\n",
" <td>0.973100</td>\n",
" <td>-4.600324</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>EMP2\\204975_at</td>\n",
" <td>1.187015</td>\n",
" <td>0.468782</td>\n",
" <td>0.641025</td>\n",
" <td>-4.599176</td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
" <td>LHFP\\218656_s_at</td>\n",
" <td>1.000603</td>\n",
" <td>0.474785</td>\n",
" <td>0.636767</td>\n",
" <td>-4.599146</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18</th>\n",
" <td>SNCAIP\\237834_at</td>\n",
" <td>0.056520</td>\n",
" <td>0.079546</td>\n",
" <td>0.936879</td>\n",
" <td>-4.600297</td>\n",
" </tr>\n",
" <tr>\n",
" <th>19</th>\n",
" <td>RDH8\\220683_at</td>\n",
" <td>-0.150771</td>\n",
" <td>-0.153581</td>\n",
" <td>0.878486</td>\n",
" <td>-4.600206</td>\n",
" </tr>\n",
" <tr>\n",
" <th>20</th>\n",
" <td>SRSF4\\239512_at</td>\n",
" <td>0.312302</td>\n",
" <td>0.184059</td>\n",
" <td>0.854625</td>\n",
" <td>-4.600152</td>\n",
" </tr>\n",
" <tr>\n",
" <th>21</th>\n",
" <td>ACTB\\213867_x_at</td>\n",
" <td>0.685520</td>\n",
" <td>0.238904</td>\n",
" <td>0.812043</td>\n",
" <td>-4.600030</td>\n",
" </tr>\n",
" <tr>\n",
" <th>22</th>\n",
" <td>FAM182B\\215487_x_at</td>\n",
" <td>0.407109</td>\n",
" <td>0.504831</td>\n",
" <td>0.615637</td>\n",
" <td>-4.598992</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23</th>\n",
" <td>C6orf108\\213871_s_at</td>\n",
" <td>-0.018360</td>\n",
" <td>-0.028788</td>\n",
" <td>0.977135</td>\n",
" <td>-4.600326</td>\n",
" </tr>\n",
" <tr>\n",
" <th>24</th>\n",
" <td>CSRNP2\\225042_s_at</td>\n",
" <td>0.401834</td>\n",
" <td>0.290746</td>\n",
" <td>0.772308</td>\n",
" <td>-4.599885</td>\n",
" </tr>\n",
" <tr>\n",
" <th>25</th>\n",
" <td>SLCO2B1\\203473_at</td>\n",
" <td>0.729965</td>\n",
" <td>0.363953</td>\n",
" <td>0.717249</td>\n",
" <td>-4.599633</td>\n",
" </tr>\n",
" <tr>\n",
" <th>26</th>\n",
" <td>MYNN\\237510_at</td>\n",
" <td>-0.254418</td>\n",
" <td>-0.284690</td>\n",
" <td>0.776921</td>\n",
" <td>-4.599904</td>\n",
" </tr>\n",
" <tr>\n",
" <th>27</th>\n",
" <td>NAP1L1\\208752_x_at</td>\n",
" <td>0.832706</td>\n",
" <td>0.352684</td>\n",
" <td>0.725635</td>\n",
" <td>-4.599676</td>\n",
" </tr>\n",
" <tr>\n",
" <th>28</th>\n",
" <td>ADAM28\\205997_at</td>\n",
" <td>0.750291</td>\n",
" <td>0.635362</td>\n",
" <td>0.527752</td>\n",
" <td>-4.598216</td>\n",
" </tr>\n",
" <tr>\n",
" <th>29</th>\n",
" <td>LOC100507248\\235236_at</td>\n",
" <td>-0.428787</td>\n",
" <td>-0.580283</td>\n",
" <td>0.564026</td>\n",
" <td>-4.598565</td>\n",
" </tr>\n",
" <tr>\n",
" <th>30</th>\n",
" <td>PHF8\\238837_at</td>\n",
" <td>0.085134</td>\n",
" <td>0.163629</td>\n",
" <td>0.870606</td>\n",
" <td>-4.600189</td>\n",
" </tr>\n",
" <tr>\n",
" <th>31</th>\n",
" <td>C9orf96\\1554787_at</td>\n",
" <td>-0.182682</td>\n",
" <td>-0.258592</td>\n",
" <td>0.796888</td>\n",
" <td>-4.599978</td>\n",
" </tr>\n",
" <tr>\n",
" <th>32</th>\n",
" <td>TNPO2\\210585_s_at</td>\n",
" <td>0.602312</td>\n",
" <td>0.766452</td>\n",
" <td>0.446591</td>\n",
" <td>-4.597263</td>\n",
" </tr>\n",
" <tr>\n",
" <th>33</th>\n",
" <td>FLJ31485\\239569_at</td>\n",
" <td>0.462034</td>\n",
" <td>0.482868</td>\n",
" <td>0.631051</td>\n",
" <td>-4.599106</td>\n",
" </tr>\n",
" <tr>\n",
" <th>34</th>\n",
" <td>PUM1\\201164_s_at</td>\n",
" <td>0.771907</td>\n",
" <td>0.393178</td>\n",
" <td>0.695665</td>\n",
" <td>-4.599517</td>\n",
" </tr>\n",
" <tr>\n",
" <th>35</th>\n",
" <td>COX4I1\\202698_x_at</td>\n",
" <td>0.889904</td>\n",
" <td>0.365176</td>\n",
" <td>0.716341</td>\n",
" <td>-4.599629</td>\n",
" </tr>\n",
" <tr>\n",
" <th>36</th>\n",
" <td>IZUMO4\\215734_at</td>\n",
" <td>0.551718</td>\n",
" <td>0.557249</td>\n",
" <td>0.579554</td>\n",
" <td>-4.598701</td>\n",
" </tr>\n",
" <tr>\n",
" <th>37</th>\n",
" <td>TPSAB1\\216485_s_at</td>\n",
" <td>0.304421</td>\n",
" <td>0.581178</td>\n",
" <td>0.563427</td>\n",
" <td>-4.598559</td>\n",
" </tr>\n",
" <tr>\n",
" <th>38</th>\n",
" <td>LMAN1L\\220420_at</td>\n",
" <td>-0.878393</td>\n",
" <td>-1.647269</td>\n",
" <td>0.105043</td>\n",
" <td>-4.586668</td>\n",
" </tr>\n",
" <tr>\n",
" <th>39</th>\n",
" <td>LY6K\\223687_s_at</td>\n",
" <td>0.668165</td>\n",
" <td>0.722964</td>\n",
" <td>0.472678</td>\n",
" <td>-4.597598</td>\n",
" </tr>\n",
" <tr>\n",
" <th>40</th>\n",
" <td>ACAD10\\238655_at</td>\n",
" <td>0.102328</td>\n",
" <td>0.098604</td>\n",
" <td>0.921801</td>\n",
" <td>-4.600279</td>\n",
" </tr>\n",
" <tr>\n",
" <th>41</th>\n",
" <td>TIMM22\\219184_x_at</td>\n",
" <td>0.502821</td>\n",
" <td>0.370580</td>\n",
" <td>0.712333</td>\n",
" <td>-4.599608</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42</th>\n",
" <td>HUS1\\217618_x_at</td>\n",
" <td>0.101851</td>\n",
" <td>0.084376</td>\n",
" <td>0.933055</td>\n",
" <td>-4.600293</td>\n",
" </tr>\n",
" <tr>\n",
" <th>43</th>\n",
" <td>EPHA7\\206852_at</td>\n",
" <td>0.224332</td>\n",
" <td>0.318597</td>\n",
" <td>0.751204</td>\n",
" <td>-4.599796</td>\n",
" </tr>\n",
" <tr>\n",
" <th>44</th>\n",
" <td>CSH1\\208069_x_at</td>\n",
" <td>0.452654</td>\n",
" <td>1.087883</td>\n",
" <td>0.281256</td>\n",
" <td>-4.594215</td>\n",
" </tr>\n",
" <tr>\n",
" <th>45</th>\n",
" <td>FMNL2\\242665_at</td>\n",
" <td>0.814379</td>\n",
" <td>0.634494</td>\n",
" <td>0.528314</td>\n",
" <td>-4.598222</td>\n",
" </tr>\n",
" <tr>\n",
" <th>46</th>\n",
" <td>PUS3\\221277_s_at</td>\n",
" <td>0.706315</td>\n",
" <td>0.472398</td>\n",
" <td>0.638458</td>\n",
" <td>-4.599158</td>\n",
" </tr>\n",
" <tr>\n",
" <th>47</th>\n",
" <td>CELF4\\231220_at</td>\n",
" <td>0.307643</td>\n",
" <td>0.600501</td>\n",
" <td>0.550569</td>\n",
" <td>-4.598440</td>\n",
" </tr>\n",
" <tr>\n",
" <th>48</th>\n",
" <td>RBM6\\228030_at</td>\n",
" <td>0.582032</td>\n",
" <td>0.291114</td>\n",
" <td>0.772028</td>\n",
" <td>-4.599884</td>\n",
" </tr>\n",
" <tr>\n",
" <th>49</th>\n",
" <td>AVIL\\233333_x_at</td>\n",
" <td>0.289393</td>\n",
" <td>0.205224</td>\n",
" <td>0.838133</td>\n",
" <td>-4.600109</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42399</th>\n",
" <td>MON1B\\233557_s_at</td>\n",
" <td>0.356762</td>\n",
" <td>0.239027</td>\n",
" <td>0.811948</td>\n",
" <td>-4.600029</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42400</th>\n",
" <td>CLLU1\\1558185_at</td>\n",
" <td>0.295150</td>\n",
" <td>0.447277</td>\n",
" <td>0.656382</td>\n",
" <td>-4.599279</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42401</th>\n",
" <td>KTN1\\214709_s_at</td>\n",
" <td>0.887451</td>\n",
" <td>0.401390</td>\n",
" <td>0.689644</td>\n",
" <td>-4.599483</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42402</th>\n",
" <td>KRTAP4-7\\216810_at</td>\n",
" <td>-0.367947</td>\n",
" <td>-0.538408</td>\n",
" <td>0.592406</td>\n",
" <td>-4.598809</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42403</th>\n",
" <td>RBKS\\219222_at</td>\n",
" <td>-0.042483</td>\n",
" <td>-0.033844</td>\n",
" <td>0.973121</td>\n",
" <td>-4.600324</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42404</th>\n",
" <td>LOC100506621\\227061_at</td>\n",
" <td>0.274594</td>\n",
" <td>0.161521</td>\n",
" <td>0.872258</td>\n",
" <td>-4.600193</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42405</th>\n",
" <td>CCDC67\\1554071_at</td>\n",
" <td>-0.495979</td>\n",
" <td>-0.769797</td>\n",
" <td>0.444620</td>\n",
" <td>-4.597237</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42406</th>\n",
" <td>MCM9\\219673_at</td>\n",
" <td>0.571932</td>\n",
" <td>0.429359</td>\n",
" <td>0.669291</td>\n",
" <td>-4.599361</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42407</th>\n",
" <td>LOC730101\\213248_at</td>\n",
" <td>0.662087</td>\n",
" <td>0.530913</td>\n",
" <td>0.597555</td>\n",
" <td>-4.598851</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42408</th>\n",
" <td>LOC100508546\\244037_at</td>\n",
" <td>1.635056</td>\n",
" <td>1.727084</td>\n",
" <td>0.089605</td>\n",
" <td>-4.585379</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42409</th>\n",
" <td>RNPS1\\200060_s_at</td>\n",
" <td>0.683944</td>\n",
" <td>0.338790</td>\n",
" <td>0.736021</td>\n",
" <td>-4.599726</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42410</th>\n",
" <td>C8orf74\\1569246_a_at</td>\n",
" <td>-0.000976</td>\n",
" <td>-0.001088</td>\n",
" <td>0.999136</td>\n",
" <td>-4.600331</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42411</th>\n",
" <td>UTP14C\\203614_at</td>\n",
" <td>0.960350</td>\n",
" <td>0.524120</td>\n",
" <td>0.602241</td>\n",
" <td>-4.598888</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42412</th>\n",
" <td>RHEB\\201452_at</td>\n",
" <td>-0.141799</td>\n",
" <td>-0.148466</td>\n",
" <td>0.882502</td>\n",
" <td>-4.600214</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42413</th>\n",
" <td>CXCL16\\223454_at</td>\n",
" <td>0.476846</td>\n",
" <td>0.246033</td>\n",
" <td>0.806546</td>\n",
" <td>-4.600012</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42414</th>\n",
" <td>PSPC1\\218371_s_at</td>\n",
" <td>0.860790</td>\n",
" <td>0.546557</td>\n",
" <td>0.586831</td>\n",
" <td>-4.598763</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42415</th>\n",
" <td>SIK3\\213034_at</td>\n",
" <td>0.482629</td>\n",
" <td>0.281011</td>\n",
" <td>0.779726</td>\n",
" <td>-4.599915</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42416</th>\n",
" <td>ACOT9\\221641_s_at</td>\n",
" <td>0.538855</td>\n",
" <td>0.292022</td>\n",
" <td>0.771337</td>\n",
" <td>-4.599881</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42417</th>\n",
" <td>KIAA1661\\215943_at</td>\n",
" <td>0.322528</td>\n",
" <td>0.448626</td>\n",
" <td>0.655414</td>\n",
" <td>-4.599273</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42418</th>\n",
" <td>STEAP2\\225871_at</td>\n",
" <td>0.488423</td>\n",
" <td>0.317957</td>\n",
" <td>0.751687</td>\n",
" <td>-4.599798</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42419</th>\n",
" <td>AKAP5\\207800_at</td>\n",
" <td>0.867480</td>\n",
" <td>1.392526</td>\n",
" <td>0.169208</td>\n",
" <td>-4.590438</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42420</th>\n",
" <td>C1orf57\\223272_s_at</td>\n",
" <td>1.061639</td>\n",
" <td>0.698401</td>\n",
" <td>0.487785</td>\n",
" <td>-4.597779</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42421</th>\n",
" <td>C7orf30\\226385_s_at</td>\n",
" <td>0.736595</td>\n",
" <td>0.366183</td>\n",
" <td>0.715593</td>\n",
" <td>-4.599625</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42422</th>\n",
" <td>BAX\\208478_s_at</td>\n",
" <td>0.316187</td>\n",
" <td>0.257996</td>\n",
" <td>0.797345</td>\n",
" <td>-4.599980</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42423</th>\n",
" <td>MAN1C1\\218918_at</td>\n",
" <td>0.438300</td>\n",
" <td>0.288937</td>\n",
" <td>0.773685</td>\n",
" <td>-4.599891</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42424</th>\n",
" <td>SGSM3\\214779_s_at</td>\n",
" <td>0.636825</td>\n",
" <td>0.455855</td>\n",
" <td>0.650238</td>\n",
" <td>-4.599238</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42425</th>\n",
" <td>LOC100508009\\231516_at</td>\n",
" <td>-0.632829</td>\n",
" <td>-1.335501</td>\n",
" <td>0.187057</td>\n",
" <td>-4.591208</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42426</th>\n",
" <td>ASCL3\\221161_at</td>\n",
" <td>-0.296944</td>\n",
" <td>-0.396476</td>\n",
" <td>0.693245</td>\n",
" <td>-4.599504</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42427</th>\n",
" <td>DALRD3\\221934_s_at</td>\n",
" <td>0.815617</td>\n",
" <td>0.545451</td>\n",
" <td>0.587586</td>\n",
" <td>-4.598769</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42428</th>\n",
" <td>DAPK2\\206324_s_at</td>\n",
" <td>0.617438</td>\n",
" <td>0.434248</td>\n",
" <td>0.665759</td>\n",
" <td>-4.599339</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42429</th>\n",
" <td>NUP155\\206550_s_at</td>\n",
" <td>0.735216</td>\n",
" <td>0.565273</td>\n",
" <td>0.574122</td>\n",
" <td>-4.598654</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42430</th>\n",
" <td>TMF1\\215855_s_at</td>\n",
" <td>0.290174</td>\n",
" <td>0.198452</td>\n",
" <td>0.843402</td>\n",
" <td>-4.600123</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42431</th>\n",
" <td>LOC100505584\\216336_x_at</td>\n",
" <td>0.184588</td>\n",
" <td>0.086769</td>\n",
" <td>0.931161</td>\n",
" <td>-4.600291</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42432</th>\n",
" <td>ARID1B\\1566990_x_at</td>\n",
" <td>0.322959</td>\n",
" <td>0.238363</td>\n",
" <td>0.812460</td>\n",
" <td>-4.600031</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42433</th>\n",
" <td>LOC100287105\\1570171_at</td>\n",
" <td>0.347364</td>\n",
" <td>0.344713</td>\n",
" <td>0.731587</td>\n",
" <td>-4.599705</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42434</th>\n",
" <td>UTRN\\225093_at</td>\n",
" <td>0.826417</td>\n",
" <td>0.383918</td>\n",
" <td>0.702477</td>\n",
" <td>-4.599555</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42435</th>\n",
" <td>HIST3H3\\208572_at</td>\n",
" <td>0.466194</td>\n",
" <td>0.786881</td>\n",
" <td>0.434633</td>\n",
" <td>-4.597099</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42436</th>\n",
" <td>ZNF316\\227170_at</td>\n",
" <td>0.308429</td>\n",
" <td>0.274918</td>\n",
" <td>0.784380</td>\n",
" <td>-4.599932</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42437</th>\n",
" <td>ETV6\\205585_at</td>\n",
" <td>0.196758</td>\n",
" <td>0.179311</td>\n",
" <td>0.858334</td>\n",
" <td>-4.600161</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42438</th>\n",
" <td>LOC400550\\243059_at</td>\n",
" <td>0.284004</td>\n",
" <td>0.239238</td>\n",
" <td>0.811785</td>\n",
" <td>-4.600029</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42439</th>\n",
" <td>B3GAT2\\234146_at</td>\n",
" <td>-0.141648</td>\n",
" <td>-0.238679</td>\n",
" <td>0.812216</td>\n",
" <td>-4.600030</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42440</th>\n",
" <td>HMGB4\\230473_s_at</td>\n",
" <td>-0.062882</td>\n",
" <td>-0.098254</td>\n",
" <td>0.922078</td>\n",
" <td>-4.600280</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42441</th>\n",
" <td>CMTM6\\217947_at</td>\n",
" <td>0.661108</td>\n",
" <td>0.279330</td>\n",
" <td>0.781009</td>\n",
" <td>-4.599920</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42442</th>\n",
" <td>BRAP\\209922_at</td>\n",
" <td>0.570144</td>\n",
" <td>0.577189</td>\n",
" <td>0.566100</td>\n",
" <td>-4.598583</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42443</th>\n",
" <td>BARD1\\205345_at</td>\n",
" <td>0.695383</td>\n",
" <td>0.482240</td>\n",
" <td>0.631494</td>\n",
" <td>-4.599109</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42444</th>\n",
" <td>MR1\\207565_s_at</td>\n",
" <td>0.311217</td>\n",
" <td>0.227616</td>\n",
" <td>0.820765</td>\n",
" <td>-4.600057</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42445</th>\n",
" <td>SORT1\\212797_at</td>\n",
" <td>0.239672</td>\n",
" <td>0.171783</td>\n",
" <td>0.864221</td>\n",
" <td>-4.600175</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42446</th>\n",
" <td>FLJ31485\\243351_at</td>\n",
" <td>0.374568</td>\n",
" <td>0.357662</td>\n",
" <td>0.721927</td>\n",
" <td>-4.599657</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42447</th>\n",
" <td>BPI\\205557_at</td>\n",
" <td>-0.506693</td>\n",
" <td>-0.641504</td>\n",
" <td>0.523784</td>\n",
" <td>-4.598175</td>\n",
" </tr>\n",
" <tr>\n",
" <th>42448</th>\n",
" <td>CECR3\\1564352_at</td>\n",
" <td>-0.170982</td>\n",
" <td>-0.191725</td>\n",
" <td>0.848643</td>\n",
" <td>-4.600137</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>42449 rows × 5 columns</p>\n",
"</div>"
],
"text/plain": [
" probe log_fc t p_value b\n",
"0 KIAA1377\\235956_at 0.879185 0.576089 0.566838 -4.598590\n",
"1 ZNF358\\226260_x_at 0.516999 0.481906 0.631730 -4.599110\n",
"2 GPR135\\214503_x_at -0.037486 -0.105517 0.916339 -4.600272\n",
"3 GPATCH2\\242224_at 0.245595 0.215820 0.829904 -4.600085\n",
"4 RPL24\\214143_x_at 1.012177 0.364221 0.717050 -4.599632\n",
"5 PALM2\\1554640_at 0.198167 0.165797 0.868907 -4.600186\n",
"6 LOC339316\\242084_at 0.001682 0.003089 0.997546 -4.600330\n",
"7 FECH\\203115_at 0.895703 0.707561 0.482120 -4.597713\n",
"8 KCNJ9\\207527_at 0.148250 0.182965 0.855479 -4.600154\n",
"9 C21orf96\\220918_at 0.286274 0.241679 0.809902 -4.600023\n",
"10 SAT2\\225272_at 0.785265 0.435954 0.664528 -4.599331\n",
"11 EHD1\\209038_s_at 0.858592 0.767820 0.445785 -4.597252\n",
"12 CBLB\\208348_s_at 0.376908 0.575643 0.567137 -4.598593\n",
"13 C20orf85\\229542_at 1.120739 0.718556 0.475370 -4.597631\n",
"14 UGGT1\\218257_s_at 0.220018 0.175489 0.861321 -4.600168\n",
"15 LOC283585\\1561442_at -0.028199 -0.033870 0.973100 -4.600324\n",
"16 EMP2\\204975_at 1.187015 0.468782 0.641025 -4.599176\n",
"17 LHFP\\218656_s_at 1.000603 0.474785 0.636767 -4.599146\n",
"18 SNCAIP\\237834_at 0.056520 0.079546 0.936879 -4.600297\n",
"19 RDH8\\220683_at -0.150771 -0.153581 0.878486 -4.600206\n",
"20 SRSF4\\239512_at 0.312302 0.184059 0.854625 -4.600152\n",
"21 ACTB\\213867_x_at 0.685520 0.238904 0.812043 -4.600030\n",
"22 FAM182B\\215487_x_at 0.407109 0.504831 0.615637 -4.598992\n",
"23 C6orf108\\213871_s_at -0.018360 -0.028788 0.977135 -4.600326\n",
"24 CSRNP2\\225042_s_at 0.401834 0.290746 0.772308 -4.599885\n",
"25 SLCO2B1\\203473_at 0.729965 0.363953 0.717249 -4.599633\n",
"26 MYNN\\237510_at -0.254418 -0.284690 0.776921 -4.599904\n",
"27 NAP1L1\\208752_x_at 0.832706 0.352684 0.725635 -4.599676\n",
"28 ADAM28\\205997_at 0.750291 0.635362 0.527752 -4.598216\n",
"29 LOC100507248\\235236_at -0.428787 -0.580283 0.564026 -4.598565\n",
"30 PHF8\\238837_at 0.085134 0.163629 0.870606 -4.600189\n",
"31 C9orf96\\1554787_at -0.182682 -0.258592 0.796888 -4.599978\n",
"32 TNPO2\\210585_s_at 0.602312 0.766452 0.446591 -4.597263\n",
"33 FLJ31485\\239569_at 0.462034 0.482868 0.631051 -4.599106\n",
"34 PUM1\\201164_s_at 0.771907 0.393178 0.695665 -4.599517\n",
"35 COX4I1\\202698_x_at 0.889904 0.365176 0.716341 -4.599629\n",
"36 IZUMO4\\215734_at 0.551718 0.557249 0.579554 -4.598701\n",
"37 TPSAB1\\216485_s_at 0.304421 0.581178 0.563427 -4.598559\n",
"38 LMAN1L\\220420_at -0.878393 -1.647269 0.105043 -4.586668\n",
"39 LY6K\\223687_s_at 0.668165 0.722964 0.472678 -4.597598\n",
"40 ACAD10\\238655_at 0.102328 0.098604 0.921801 -4.600279\n",
"41 TIMM22\\219184_x_at 0.502821 0.370580 0.712333 -4.599608\n",
"42 HUS1\\217618_x_at 0.101851 0.084376 0.933055 -4.600293\n",
"43 EPHA7\\206852_at 0.224332 0.318597 0.751204 -4.599796\n",
"44 CSH1\\208069_x_at 0.452654 1.087883 0.281256 -4.594215\n",
"45 FMNL2\\242665_at 0.814379 0.634494 0.528314 -4.598222\n",
"46 PUS3\\221277_s_at 0.706315 0.472398 0.638458 -4.599158\n",
"47 CELF4\\231220_at 0.307643 0.600501 0.550569 -4.598440\n",
"48 RBM6\\228030_at 0.582032 0.291114 0.772028 -4.599884\n",
"49 AVIL\\233333_x_at 0.289393 0.205224 0.838133 -4.600109\n",
"... ... ... ... ... ...\n",
"42399 MON1B\\233557_s_at 0.356762 0.239027 0.811948 -4.600029\n",
"42400 CLLU1\\1558185_at 0.295150 0.447277 0.656382 -4.599279\n",
"42401 KTN1\\214709_s_at 0.887451 0.401390 0.689644 -4.599483\n",
"42402 KRTAP4-7\\216810_at -0.367947 -0.538408 0.592406 -4.598809\n",
"42403 RBKS\\219222_at -0.042483 -0.033844 0.973121 -4.600324\n",
"42404 LOC100506621\\227061_at 0.274594 0.161521 0.872258 -4.600193\n",
"42405 CCDC67\\1554071_at -0.495979 -0.769797 0.444620 -4.597237\n",
"42406 MCM9\\219673_at 0.571932 0.429359 0.669291 -4.599361\n",
"42407 LOC730101\\213248_at 0.662087 0.530913 0.597555 -4.598851\n",
"42408 LOC100508546\\244037_at 1.635056 1.727084 0.089605 -4.585379\n",
"42409 RNPS1\\200060_s_at 0.683944 0.338790 0.736021 -4.599726\n",
"42410 C8orf74\\1569246_a_at -0.000976 -0.001088 0.999136 -4.600331\n",
"42411 UTP14C\\203614_at 0.960350 0.524120 0.602241 -4.598888\n",
"42412 RHEB\\201452_at -0.141799 -0.148466 0.882502 -4.600214\n",
"42413 CXCL16\\223454_at 0.476846 0.246033 0.806546 -4.600012\n",
"42414 PSPC1\\218371_s_at 0.860790 0.546557 0.586831 -4.598763\n",
"42415 SIK3\\213034_at 0.482629 0.281011 0.779726 -4.599915\n",
"42416 ACOT9\\221641_s_at 0.538855 0.292022 0.771337 -4.599881\n",
"42417 KIAA1661\\215943_at 0.322528 0.448626 0.655414 -4.599273\n",
"42418 STEAP2\\225871_at 0.488423 0.317957 0.751687 -4.599798\n",
"42419 AKAP5\\207800_at 0.867480 1.392526 0.169208 -4.590438\n",
"42420 C1orf57\\223272_s_at 1.061639 0.698401 0.487785 -4.597779\n",
"42421 C7orf30\\226385_s_at 0.736595 0.366183 0.715593 -4.599625\n",
"42422 BAX\\208478_s_at 0.316187 0.257996 0.797345 -4.599980\n",
"42423 MAN1C1\\218918_at 0.438300 0.288937 0.773685 -4.599891\n",
"42424 SGSM3\\214779_s_at 0.636825 0.455855 0.650238 -4.599238\n",
"42425 LOC100508009\\231516_at -0.632829 -1.335501 0.187057 -4.591208\n",
"42426 ASCL3\\221161_at -0.296944 -0.396476 0.693245 -4.599504\n",
"42427 DALRD3\\221934_s_at 0.815617 0.545451 0.587586 -4.598769\n",
"42428 DAPK2\\206324_s_at 0.617438 0.434248 0.665759 -4.599339\n",
"42429 NUP155\\206550_s_at 0.735216 0.565273 0.574122 -4.598654\n",
"42430 TMF1\\215855_s_at 0.290174 0.198452 0.843402 -4.600123\n",
"42431 LOC100505584\\216336_x_at 0.184588 0.086769 0.931161 -4.600291\n",
"42432 ARID1B\\1566990_x_at 0.322959 0.238363 0.812460 -4.600031\n",
"42433 LOC100287105\\1570171_at 0.347364 0.344713 0.731587 -4.599705\n",
"42434 UTRN\\225093_at 0.826417 0.383918 0.702477 -4.599555\n",
"42435 HIST3H3\\208572_at 0.466194 0.786881 0.434633 -4.597099\n",
"42436 ZNF316\\227170_at 0.308429 0.274918 0.784380 -4.599932\n",
"42437 ETV6\\205585_at 0.196758 0.179311 0.858334 -4.600161\n",
"42438 LOC400550\\243059_at 0.284004 0.239238 0.811785 -4.600029\n",
"42439 B3GAT2\\234146_at -0.141648 -0.238679 0.812216 -4.600030\n",
"42440 HMGB4\\230473_s_at -0.062882 -0.098254 0.922078 -4.600280\n",
"42441 CMTM6\\217947_at 0.661108 0.279330 0.781009 -4.599920\n",
"42442 BRAP\\209922_at 0.570144 0.577189 0.566100 -4.598583\n",
"42443 BARD1\\205345_at 0.695383 0.482240 0.631494 -4.599109\n",
"42444 MR1\\207565_s_at 0.311217 0.227616 0.820765 -4.600057\n",
"42445 SORT1\\212797_at 0.239672 0.171783 0.864221 -4.600175\n",
"42446 FLJ31485\\243351_at 0.374568 0.357662 0.721927 -4.599657\n",
"42447 BPI\\205557_at -0.506693 -0.641504 0.523784 -4.598175\n",
"42448 CECR3\\1564352_at -0.170982 -0.191725 0.848643 -4.600137\n",
"\n",
"[42449 rows x 5 columns]"
]
},
"execution_count": 52,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"top_fit"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Filtering results on p-value\n",
"\n",
"Back to Python....we can access **top_fit** variable because it was passed above as an \"output\" parameter to the R code. We use it to select the probes below a specific p-value threshold."
]
},
{
"cell_type": "code",
"execution_count": 57,
"metadata": {
"collapsed": false,
"scrolled": true
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>log_fc</th>\n",
" <th>t</th>\n",
" <th>p_value</th>\n",
" <th>b</th>\n",
" </tr>\n",
" <tr>\n",
" <th>probe</th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>IL1F8\\224230_at</th>\n",
" <td>-1.546104</td>\n",
" <td>-3.449570</td>\n",
" <td>0.001067</td>\n",
" <td>-4.548413</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC400590\\1560992_at</th>\n",
" <td>2.197704</td>\n",
" <td>3.434648</td>\n",
" <td>0.001117</td>\n",
" <td>-4.548785</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ANGEL1\\244685_at</th>\n",
" <td>-1.178030</td>\n",
" <td>-2.807717</td>\n",
" <td>0.006833</td>\n",
" <td>-4.563804</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GRK7\\1552929_at</th>\n",
" <td>1.679992</td>\n",
" <td>2.562875</td>\n",
" <td>0.013065</td>\n",
" <td>-4.569267</td>\n",
" </tr>\n",
" <tr>\n",
" <th>FLJ33996\\237790_at</th>\n",
" <td>1.203864</td>\n",
" <td>2.546120</td>\n",
" <td>0.013639</td>\n",
" <td>-4.569630</td>\n",
" </tr>\n",
" <tr>\n",
" <th>POSTN\\214981_at</th>\n",
" <td>2.156220</td>\n",
" <td>2.520897</td>\n",
" <td>0.014548</td>\n",
" <td>-4.570174</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100507153\\1568762_at</th>\n",
" <td>1.538902</td>\n",
" <td>2.507401</td>\n",
" <td>0.015056</td>\n",
" <td>-4.570464</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GPR17\\206190_at</th>\n",
" <td>1.318751</td>\n",
" <td>2.456309</td>\n",
" <td>0.017129</td>\n",
" <td>-4.571554</td>\n",
" </tr>\n",
" <tr>\n",
" <th>TTC39A\\217101_at</th>\n",
" <td>1.249650</td>\n",
" <td>2.448672</td>\n",
" <td>0.017460</td>\n",
" <td>-4.571715</td>\n",
" </tr>\n",
" <tr>\n",
" <th>RNF141\\1565546_at</th>\n",
" <td>1.546828</td>\n",
" <td>2.437364</td>\n",
" <td>0.017960</td>\n",
" <td>-4.571954</td>\n",
" </tr>\n",
" <tr>\n",
" <th>MAF\\1566323_at</th>\n",
" <td>-1.440637</td>\n",
" <td>-2.433496</td>\n",
" <td>0.018134</td>\n",
" <td>-4.572036</td>\n",
" </tr>\n",
" <tr>\n",
" <th>DPF3\\235357_at</th>\n",
" <td>-1.212370</td>\n",
" <td>-2.400648</td>\n",
" <td>0.019676</td>\n",
" <td>-4.572725</td>\n",
" </tr>\n",
" <tr>\n",
" <th>METAP1D\\1565755_at</th>\n",
" <td>1.510195</td>\n",
" <td>2.399407</td>\n",
" <td>0.019736</td>\n",
" <td>-4.572750</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ZNF780B\\214899_at</th>\n",
" <td>1.644326</td>\n",
" <td>2.396825</td>\n",
" <td>0.019863</td>\n",
" <td>-4.572804</td>\n",
" </tr>\n",
" <tr>\n",
" <th>RUNX1T1\\216831_s_at</th>\n",
" <td>2.096988</td>\n",
" <td>2.390294</td>\n",
" <td>0.020185</td>\n",
" <td>-4.572940</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GFRA2\\205722_s_at</th>\n",
" <td>1.386836</td>\n",
" <td>2.371531</td>\n",
" <td>0.021139</td>\n",
" <td>-4.573330</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100288139\\234426_x_at</th>\n",
" <td>1.580194</td>\n",
" <td>2.351281</td>\n",
" <td>0.022214</td>\n",
" <td>-4.573749</td>\n",
" </tr>\n",
" <tr>\n",
" <th>C2orf14\\224278_at</th>\n",
" <td>-1.270161</td>\n",
" <td>-2.346501</td>\n",
" <td>0.022474</td>\n",
" <td>-4.573847</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOXL4\\1570219_at</th>\n",
" <td>-1.320024</td>\n",
" <td>-2.322838</td>\n",
" <td>0.023805</td>\n",
" <td>-4.574333</td>\n",
" </tr>\n",
" <tr>\n",
" <th>IGHG1\\216892_at</th>\n",
" <td>-1.353338</td>\n",
" <td>-2.304121</td>\n",
" <td>0.024907</td>\n",
" <td>-4.574714</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PKLR\\210451_at</th>\n",
" <td>-0.951392</td>\n",
" <td>-2.302312</td>\n",
" <td>0.025016</td>\n",
" <td>-4.574751</td>\n",
" </tr>\n",
" <tr>\n",
" <th>TRAF5\\1569861_at</th>\n",
" <td>-1.419547</td>\n",
" <td>-2.296200</td>\n",
" <td>0.025387</td>\n",
" <td>-4.574875</td>\n",
" </tr>\n",
" <tr>\n",
" <th>DNAH14\\1567861_at</th>\n",
" <td>1.368343</td>\n",
" <td>2.294568</td>\n",
" <td>0.025487</td>\n",
" <td>-4.574908</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GRIA3\\230144_at</th>\n",
" <td>1.585759</td>\n",
" <td>2.250786</td>\n",
" <td>0.028300</td>\n",
" <td>-4.575791</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SLC38A10\\1563226_at</th>\n",
" <td>1.611960</td>\n",
" <td>2.246147</td>\n",
" <td>0.028613</td>\n",
" <td>-4.575883</td>\n",
" </tr>\n",
" <tr>\n",
" <th>MARCH7\\1557703_at</th>\n",
" <td>1.264078</td>\n",
" <td>2.235305</td>\n",
" <td>0.029358</td>\n",
" <td>-4.576100</td>\n",
" </tr>\n",
" <tr>\n",
" <th>NCOA3\\1562439_at</th>\n",
" <td>1.279497</td>\n",
" <td>2.219504</td>\n",
" <td>0.030475</td>\n",
" <td>-4.576414</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100287689\\243665_s_at</th>\n",
" <td>1.315087</td>\n",
" <td>2.217997</td>\n",
" <td>0.030583</td>\n",
" <td>-4.576444</td>\n",
" </tr>\n",
" <tr>\n",
" <th>MAGIX\\219965_s_at</th>\n",
" <td>1.666859</td>\n",
" <td>2.213778</td>\n",
" <td>0.030888</td>\n",
" <td>-4.576528</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC643763\\1558387_at</th>\n",
" <td>-1.716835</td>\n",
" <td>-2.193242</td>\n",
" <td>0.032413</td>\n",
" <td>-4.576933</td>\n",
" </tr>\n",
" <tr>\n",
" <th>UBR4\\231889_at</th>\n",
" <td>1.342234</td>\n",
" <td>2.188355</td>\n",
" <td>0.032785</td>\n",
" <td>-4.577029</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GTPBP10\\230684_at</th>\n",
" <td>1.667459</td>\n",
" <td>2.178850</td>\n",
" <td>0.033520</td>\n",
" <td>-4.577215</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ADCYAP1\\230237_at</th>\n",
" <td>-1.768758</td>\n",
" <td>-2.173114</td>\n",
" <td>0.033971</td>\n",
" <td>-4.577328</td>\n",
" </tr>\n",
" <tr>\n",
" <th>CRYBA2\\220136_s_at</th>\n",
" <td>0.787749</td>\n",
" <td>2.155419</td>\n",
" <td>0.035394</td>\n",
" <td>-4.577673</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LMTK2\\235307_at</th>\n",
" <td>-1.246947</td>\n",
" <td>-2.145262</td>\n",
" <td>0.036235</td>\n",
" <td>-4.577870</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PRO2949\\1553374_at</th>\n",
" <td>1.496370</td>\n",
" <td>2.143200</td>\n",
" <td>0.036408</td>\n",
" <td>-4.577910</td>\n",
" </tr>\n",
" <tr>\n",
" <th>C9orf130\\234429_at</th>\n",
" <td>1.169090</td>\n",
" <td>2.132408</td>\n",
" <td>0.037324</td>\n",
" <td>-4.578118</td>\n",
" </tr>\n",
" <tr>\n",
" <th>DNM3\\1558502_s_at</th>\n",
" <td>1.823855</td>\n",
" <td>2.131027</td>\n",
" <td>0.037442</td>\n",
" <td>-4.578145</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HBQ1\\220807_at</th>\n",
" <td>-0.815548</td>\n",
" <td>-2.116788</td>\n",
" <td>0.038685</td>\n",
" <td>-4.578419</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100131825\\217442_at</th>\n",
" <td>1.476831</td>\n",
" <td>2.112839</td>\n",
" <td>0.039036</td>\n",
" <td>-4.578494</td>\n",
" </tr>\n",
" <tr>\n",
" <th>IL17B\\220273_at</th>\n",
" <td>1.360296</td>\n",
" <td>2.111163</td>\n",
" <td>0.039186</td>\n",
" <td>-4.578527</td>\n",
" </tr>\n",
" <tr>\n",
" <th>MAGEB4\\207580_at</th>\n",
" <td>-1.415009</td>\n",
" <td>-2.104162</td>\n",
" <td>0.039817</td>\n",
" <td>-4.578660</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PEX26\\235098_at</th>\n",
" <td>1.422767</td>\n",
" <td>2.094647</td>\n",
" <td>0.040689</td>\n",
" <td>-4.578842</td>\n",
" </tr>\n",
" <tr>\n",
" <th>POFUT2\\207448_at</th>\n",
" <td>-0.987136</td>\n",
" <td>-2.091314</td>\n",
" <td>0.040998</td>\n",
" <td>-4.578905</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ART1\\1570480_s_at</th>\n",
" <td>-1.162461</td>\n",
" <td>-2.081568</td>\n",
" <td>0.041915</td>\n",
" <td>-4.579091</td>\n",
" </tr>\n",
" <tr>\n",
" <th>CIT\\242872_at</th>\n",
" <td>1.527711</td>\n",
" <td>2.080893</td>\n",
" <td>0.041979</td>\n",
" <td>-4.579103</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SSX2\\210497_x_at</th>\n",
" <td>-1.218773</td>\n",
" <td>-2.079931</td>\n",
" <td>0.042070</td>\n",
" <td>-4.579122</td>\n",
" </tr>\n",
" <tr>\n",
" <th>C20orf94\\236390_at</th>\n",
" <td>1.607248</td>\n",
" <td>2.070293</td>\n",
" <td>0.042997</td>\n",
" <td>-4.579304</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SLC17A1\\1560885_x_at</th>\n",
" <td>-1.133660</td>\n",
" <td>-2.066863</td>\n",
" <td>0.043331</td>\n",
" <td>-4.579369</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PCP4\\205549_at</th>\n",
" <td>-1.410662</td>\n",
" <td>-2.061366</td>\n",
" <td>0.043871</td>\n",
" <td>-4.579472</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GOLM1\\1558248_at</th>\n",
" <td>1.361249</td>\n",
" <td>2.046192</td>\n",
" <td>0.045392</td>\n",
" <td>-4.579757</td>\n",
" </tr>\n",
" <tr>\n",
" <th>RNASE1\\217093_at</th>\n",
" <td>1.136094</td>\n",
" <td>2.037896</td>\n",
" <td>0.046243</td>\n",
" <td>-4.579913</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ZNRD1-AS\\234457_at</th>\n",
" <td>-1.297711</td>\n",
" <td>-2.036670</td>\n",
" <td>0.046369</td>\n",
" <td>-4.579935</td>\n",
" </tr>\n",
" <tr>\n",
" <th>METTL6\\1557991_at</th>\n",
" <td>1.328631</td>\n",
" <td>2.034147</td>\n",
" <td>0.046631</td>\n",
" <td>-4.579982</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC389634\\1560119_at</th>\n",
" <td>1.716840</td>\n",
" <td>2.032055</td>\n",
" <td>0.046850</td>\n",
" <td>-4.580021</td>\n",
" </tr>\n",
" <tr>\n",
" <th>IL2\\207849_at</th>\n",
" <td>-1.448060</td>\n",
" <td>-2.030678</td>\n",
" <td>0.046994</td>\n",
" <td>-4.580047</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PRLR\\211917_s_at</th>\n",
" <td>1.410709</td>\n",
" <td>2.029950</td>\n",
" <td>0.047070</td>\n",
" <td>-4.580061</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GRIK2\\1555375_at</th>\n",
" <td>-1.422374</td>\n",
" <td>-2.029393</td>\n",
" <td>0.047129</td>\n",
" <td>-4.580071</td>\n",
" </tr>\n",
" <tr>\n",
" <th>RGS20\\210138_at</th>\n",
" <td>1.453221</td>\n",
" <td>2.029172</td>\n",
" <td>0.047152</td>\n",
" <td>-4.580075</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GP5\\211525_s_at</th>\n",
" <td>-1.216566</td>\n",
" <td>-2.027948</td>\n",
" <td>0.047281</td>\n",
" <td>-4.580098</td>\n",
" </tr>\n",
" <tr>\n",
" <th>TSC2\\215624_at</th>\n",
" <td>1.636716</td>\n",
" <td>2.024535</td>\n",
" <td>0.047642</td>\n",
" <td>-4.580161</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PDE6A\\206623_at</th>\n",
" <td>1.567774</td>\n",
" <td>2.023391</td>\n",
" <td>0.047763</td>\n",
" <td>-4.580183</td>\n",
" </tr>\n",
" <tr>\n",
" <th>FAM84A\\228459_at</th>\n",
" <td>1.097656</td>\n",
" <td>2.022142</td>\n",
" <td>0.047896</td>\n",
" <td>-4.580206</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC283868\\1564683_at</th>\n",
" <td>1.313171</td>\n",
" <td>2.021121</td>\n",
" <td>0.048005</td>\n",
" <td>-4.580225</td>\n",
" </tr>\n",
" <tr>\n",
" <th>BEND6\\1568820_a_at</th>\n",
" <td>-0.943036</td>\n",
" <td>-2.019456</td>\n",
" <td>0.048183</td>\n",
" <td>-4.580256</td>\n",
" </tr>\n",
" <tr>\n",
" <th>C21orf94\\1553519_at</th>\n",
" <td>-1.175958</td>\n",
" <td>-2.016891</td>\n",
" <td>0.048458</td>\n",
" <td>-4.580303</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ACTL9\\243208_x_at</th>\n",
" <td>1.103029</td>\n",
" <td>2.010967</td>\n",
" <td>0.049099</td>\n",
" <td>-4.580413</td>\n",
" </tr>\n",
" <tr>\n",
" <th>EFCAB6\\234732_s_at</th>\n",
" <td>1.412526</td>\n",
" <td>2.006627</td>\n",
" <td>0.049574</td>\n",
" <td>-4.580493</td>\n",
" </tr>\n",
" <tr>\n",
" <th>KDSR\\222359_x_at</th>\n",
" <td>1.343963</td>\n",
" <td>2.006528</td>\n",
" <td>0.049585</td>\n",
" <td>-4.580495</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100506920\\237659_at</th>\n",
" <td>0.776889</td>\n",
" <td>2.005503</td>\n",
" <td>0.049697</td>\n",
" <td>-4.580514</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SHMT1\\231701_s_at</th>\n",
" <td>-1.117987</td>\n",
" <td>-2.004808</td>\n",
" <td>0.049774</td>\n",
" <td>-4.580527</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" log_fc t p_value b\n",
"probe \n",
"IL1F8\\224230_at -1.546104 -3.449570 0.001067 -4.548413\n",
"LOC400590\\1560992_at 2.197704 3.434648 0.001117 -4.548785\n",
"ANGEL1\\244685_at -1.178030 -2.807717 0.006833 -4.563804\n",
"GRK7\\1552929_at 1.679992 2.562875 0.013065 -4.569267\n",
"FLJ33996\\237790_at 1.203864 2.546120 0.013639 -4.569630\n",
"POSTN\\214981_at 2.156220 2.520897 0.014548 -4.570174\n",
"LOC100507153\\1568762_at 1.538902 2.507401 0.015056 -4.570464\n",
"GPR17\\206190_at 1.318751 2.456309 0.017129 -4.571554\n",
"TTC39A\\217101_at 1.249650 2.448672 0.017460 -4.571715\n",
"RNF141\\1565546_at 1.546828 2.437364 0.017960 -4.571954\n",
"MAF\\1566323_at -1.440637 -2.433496 0.018134 -4.572036\n",
"DPF3\\235357_at -1.212370 -2.400648 0.019676 -4.572725\n",
"METAP1D\\1565755_at 1.510195 2.399407 0.019736 -4.572750\n",
"ZNF780B\\214899_at 1.644326 2.396825 0.019863 -4.572804\n",
"RUNX1T1\\216831_s_at 2.096988 2.390294 0.020185 -4.572940\n",
"GFRA2\\205722_s_at 1.386836 2.371531 0.021139 -4.573330\n",
"LOC100288139\\234426_x_at 1.580194 2.351281 0.022214 -4.573749\n",
"C2orf14\\224278_at -1.270161 -2.346501 0.022474 -4.573847\n",
"LOXL4\\1570219_at -1.320024 -2.322838 0.023805 -4.574333\n",
"IGHG1\\216892_at -1.353338 -2.304121 0.024907 -4.574714\n",
"PKLR\\210451_at -0.951392 -2.302312 0.025016 -4.574751\n",
"TRAF5\\1569861_at -1.419547 -2.296200 0.025387 -4.574875\n",
"DNAH14\\1567861_at 1.368343 2.294568 0.025487 -4.574908\n",
"GRIA3\\230144_at 1.585759 2.250786 0.028300 -4.575791\n",
"SLC38A10\\1563226_at 1.611960 2.246147 0.028613 -4.575883\n",
"MARCH7\\1557703_at 1.264078 2.235305 0.029358 -4.576100\n",
"NCOA3\\1562439_at 1.279497 2.219504 0.030475 -4.576414\n",
"LOC100287689\\243665_s_at 1.315087 2.217997 0.030583 -4.576444\n",
"MAGIX\\219965_s_at 1.666859 2.213778 0.030888 -4.576528\n",
"LOC643763\\1558387_at -1.716835 -2.193242 0.032413 -4.576933\n",
"UBR4\\231889_at 1.342234 2.188355 0.032785 -4.577029\n",
"GTPBP10\\230684_at 1.667459 2.178850 0.033520 -4.577215\n",
"ADCYAP1\\230237_at -1.768758 -2.173114 0.033971 -4.577328\n",
"CRYBA2\\220136_s_at 0.787749 2.155419 0.035394 -4.577673\n",
"LMTK2\\235307_at -1.246947 -2.145262 0.036235 -4.577870\n",
"PRO2949\\1553374_at 1.496370 2.143200 0.036408 -4.577910\n",
"C9orf130\\234429_at 1.169090 2.132408 0.037324 -4.578118\n",
"DNM3\\1558502_s_at 1.823855 2.131027 0.037442 -4.578145\n",
"HBQ1\\220807_at -0.815548 -2.116788 0.038685 -4.578419\n",
"LOC100131825\\217442_at 1.476831 2.112839 0.039036 -4.578494\n",
"IL17B\\220273_at 1.360296 2.111163 0.039186 -4.578527\n",
"MAGEB4\\207580_at -1.415009 -2.104162 0.039817 -4.578660\n",
"PEX26\\235098_at 1.422767 2.094647 0.040689 -4.578842\n",
"POFUT2\\207448_at -0.987136 -2.091314 0.040998 -4.578905\n",
"ART1\\1570480_s_at -1.162461 -2.081568 0.041915 -4.579091\n",
"CIT\\242872_at 1.527711 2.080893 0.041979 -4.579103\n",
"SSX2\\210497_x_at -1.218773 -2.079931 0.042070 -4.579122\n",
"C20orf94\\236390_at 1.607248 2.070293 0.042997 -4.579304\n",
"SLC17A1\\1560885_x_at -1.133660 -2.066863 0.043331 -4.579369\n",
"PCP4\\205549_at -1.410662 -2.061366 0.043871 -4.579472\n",
"GOLM1\\1558248_at 1.361249 2.046192 0.045392 -4.579757\n",
"RNASE1\\217093_at 1.136094 2.037896 0.046243 -4.579913\n",
"ZNRD1-AS\\234457_at -1.297711 -2.036670 0.046369 -4.579935\n",
"METTL6\\1557991_at 1.328631 2.034147 0.046631 -4.579982\n",
"LOC389634\\1560119_at 1.716840 2.032055 0.046850 -4.580021\n",
"IL2\\207849_at -1.448060 -2.030678 0.046994 -4.580047\n",
"PRLR\\211917_s_at 1.410709 2.029950 0.047070 -4.580061\n",
"GRIK2\\1555375_at -1.422374 -2.029393 0.047129 -4.580071\n",
"RGS20\\210138_at 1.453221 2.029172 0.047152 -4.580075\n",
"GP5\\211525_s_at -1.216566 -2.027948 0.047281 -4.580098\n",
"TSC2\\215624_at 1.636716 2.024535 0.047642 -4.580161\n",
"PDE6A\\206623_at 1.567774 2.023391 0.047763 -4.580183\n",
"FAM84A\\228459_at 1.097656 2.022142 0.047896 -4.580206\n",
"LOC283868\\1564683_at 1.313171 2.021121 0.048005 -4.580225\n",
"BEND6\\1568820_a_at -0.943036 -2.019456 0.048183 -4.580256\n",
"C21orf94\\1553519_at -1.175958 -2.016891 0.048458 -4.580303\n",
"ACTL9\\243208_x_at 1.103029 2.010967 0.049099 -4.580413\n",
"EFCAB6\\234732_s_at 1.412526 2.006627 0.049574 -4.580493\n",
"KDSR\\222359_x_at 1.343963 2.006528 0.049585 -4.580495\n",
"LOC100506920\\237659_at 0.776889 2.005503 0.049697 -4.580514\n",
"SHMT1\\231701_s_at -1.117987 -2.004808 0.049774 -4.580527"
]
},
"execution_count": 57,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"top_probes = top_fit[top_fit.p_value < 0.05] \\\n",
" .set_index(['probe']).sort(['p_value'], ascending = True)\n",
"top_probes"
]
},
{
"cell_type": "code",
"execution_count": 58,
"metadata": {
"collapsed": false,
"scrolled": true
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>log_fc</th>\n",
" <th>t</th>\n",
" <th>p_value</th>\n",
" <th>b</th>\n",
" <th>gene_name</th>\n",
" </tr>\n",
" <tr>\n",
" <th>probe</th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>IL1F8\\224230_at</th>\n",
" <td>-1.546104</td>\n",
" <td>-3.449570</td>\n",
" <td>0.001067</td>\n",
" <td>-4.548413</td>\n",
" <td>IL1F8</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC400590\\1560992_at</th>\n",
" <td>2.197704</td>\n",
" <td>3.434648</td>\n",
" <td>0.001117</td>\n",
" <td>-4.548785</td>\n",
" <td>LOC400590</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ANGEL1\\244685_at</th>\n",
" <td>-1.178030</td>\n",
" <td>-2.807717</td>\n",
" <td>0.006833</td>\n",
" <td>-4.563804</td>\n",
" <td>ANGEL1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GRK7\\1552929_at</th>\n",
" <td>1.679992</td>\n",
" <td>2.562875</td>\n",
" <td>0.013065</td>\n",
" <td>-4.569267</td>\n",
" <td>GRK7</td>\n",
" </tr>\n",
" <tr>\n",
" <th>FLJ33996\\237790_at</th>\n",
" <td>1.203864</td>\n",
" <td>2.546120</td>\n",
" <td>0.013639</td>\n",
" <td>-4.569630</td>\n",
" <td>FLJ33996</td>\n",
" </tr>\n",
" <tr>\n",
" <th>POSTN\\214981_at</th>\n",
" <td>2.156220</td>\n",
" <td>2.520897</td>\n",
" <td>0.014548</td>\n",
" <td>-4.570174</td>\n",
" <td>POSTN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100507153\\1568762_at</th>\n",
" <td>1.538902</td>\n",
" <td>2.507401</td>\n",
" <td>0.015056</td>\n",
" <td>-4.570464</td>\n",
" <td>LOC100507153</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GPR17\\206190_at</th>\n",
" <td>1.318751</td>\n",
" <td>2.456309</td>\n",
" <td>0.017129</td>\n",
" <td>-4.571554</td>\n",
" <td>GPR17</td>\n",
" </tr>\n",
" <tr>\n",
" <th>TTC39A\\217101_at</th>\n",
" <td>1.249650</td>\n",
" <td>2.448672</td>\n",
" <td>0.017460</td>\n",
" <td>-4.571715</td>\n",
" <td>TTC39A</td>\n",
" </tr>\n",
" <tr>\n",
" <th>RNF141\\1565546_at</th>\n",
" <td>1.546828</td>\n",
" <td>2.437364</td>\n",
" <td>0.017960</td>\n",
" <td>-4.571954</td>\n",
" <td>RNF141</td>\n",
" </tr>\n",
" <tr>\n",
" <th>MAF\\1566323_at</th>\n",
" <td>-1.440637</td>\n",
" <td>-2.433496</td>\n",
" <td>0.018134</td>\n",
" <td>-4.572036</td>\n",
" <td>MAF</td>\n",
" </tr>\n",
" <tr>\n",
" <th>DPF3\\235357_at</th>\n",
" <td>-1.212370</td>\n",
" <td>-2.400648</td>\n",
" <td>0.019676</td>\n",
" <td>-4.572725</td>\n",
" <td>DPF3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>METAP1D\\1565755_at</th>\n",
" <td>1.510195</td>\n",
" <td>2.399407</td>\n",
" <td>0.019736</td>\n",
" <td>-4.572750</td>\n",
" <td>METAP1D</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ZNF780B\\214899_at</th>\n",
" <td>1.644326</td>\n",
" <td>2.396825</td>\n",
" <td>0.019863</td>\n",
" <td>-4.572804</td>\n",
" <td>ZNF780B</td>\n",
" </tr>\n",
" <tr>\n",
" <th>RUNX1T1\\216831_s_at</th>\n",
" <td>2.096988</td>\n",
" <td>2.390294</td>\n",
" <td>0.020185</td>\n",
" <td>-4.572940</td>\n",
" <td>RUNX1T1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GFRA2\\205722_s_at</th>\n",
" <td>1.386836</td>\n",
" <td>2.371531</td>\n",
" <td>0.021139</td>\n",
" <td>-4.573330</td>\n",
" <td>GFRA2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100288139\\234426_x_at</th>\n",
" <td>1.580194</td>\n",
" <td>2.351281</td>\n",
" <td>0.022214</td>\n",
" <td>-4.573749</td>\n",
" <td>LOC100288139</td>\n",
" </tr>\n",
" <tr>\n",
" <th>C2orf14\\224278_at</th>\n",
" <td>-1.270161</td>\n",
" <td>-2.346501</td>\n",
" <td>0.022474</td>\n",
" <td>-4.573847</td>\n",
" <td>C2orf14</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOXL4\\1570219_at</th>\n",
" <td>-1.320024</td>\n",
" <td>-2.322838</td>\n",
" <td>0.023805</td>\n",
" <td>-4.574333</td>\n",
" <td>LOXL4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>IGHG1\\216892_at</th>\n",
" <td>-1.353338</td>\n",
" <td>-2.304121</td>\n",
" <td>0.024907</td>\n",
" <td>-4.574714</td>\n",
" <td>IGHG1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PKLR\\210451_at</th>\n",
" <td>-0.951392</td>\n",
" <td>-2.302312</td>\n",
" <td>0.025016</td>\n",
" <td>-4.574751</td>\n",
" <td>PKLR</td>\n",
" </tr>\n",
" <tr>\n",
" <th>TRAF5\\1569861_at</th>\n",
" <td>-1.419547</td>\n",
" <td>-2.296200</td>\n",
" <td>0.025387</td>\n",
" <td>-4.574875</td>\n",
" <td>TRAF5</td>\n",
" </tr>\n",
" <tr>\n",
" <th>DNAH14\\1567861_at</th>\n",
" <td>1.368343</td>\n",
" <td>2.294568</td>\n",
" <td>0.025487</td>\n",
" <td>-4.574908</td>\n",
" <td>DNAH14</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GRIA3\\230144_at</th>\n",
" <td>1.585759</td>\n",
" <td>2.250786</td>\n",
" <td>0.028300</td>\n",
" <td>-4.575791</td>\n",
" <td>GRIA3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SLC38A10\\1563226_at</th>\n",
" <td>1.611960</td>\n",
" <td>2.246147</td>\n",
" <td>0.028613</td>\n",
" <td>-4.575883</td>\n",
" <td>SLC38A10</td>\n",
" </tr>\n",
" <tr>\n",
" <th>MARCH7\\1557703_at</th>\n",
" <td>1.264078</td>\n",
" <td>2.235305</td>\n",
" <td>0.029358</td>\n",
" <td>-4.576100</td>\n",
" <td>MARCH7</td>\n",
" </tr>\n",
" <tr>\n",
" <th>NCOA3\\1562439_at</th>\n",
" <td>1.279497</td>\n",
" <td>2.219504</td>\n",
" <td>0.030475</td>\n",
" <td>-4.576414</td>\n",
" <td>NCOA3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100287689\\243665_s_at</th>\n",
" <td>1.315087</td>\n",
" <td>2.217997</td>\n",
" <td>0.030583</td>\n",
" <td>-4.576444</td>\n",
" <td>LOC100287689</td>\n",
" </tr>\n",
" <tr>\n",
" <th>MAGIX\\219965_s_at</th>\n",
" <td>1.666859</td>\n",
" <td>2.213778</td>\n",
" <td>0.030888</td>\n",
" <td>-4.576528</td>\n",
" <td>MAGIX</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC643763\\1558387_at</th>\n",
" <td>-1.716835</td>\n",
" <td>-2.193242</td>\n",
" <td>0.032413</td>\n",
" <td>-4.576933</td>\n",
" <td>LOC643763</td>\n",
" </tr>\n",
" <tr>\n",
" <th>UBR4\\231889_at</th>\n",
" <td>1.342234</td>\n",
" <td>2.188355</td>\n",
" <td>0.032785</td>\n",
" <td>-4.577029</td>\n",
" <td>UBR4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GTPBP10\\230684_at</th>\n",
" <td>1.667459</td>\n",
" <td>2.178850</td>\n",
" <td>0.033520</td>\n",
" <td>-4.577215</td>\n",
" <td>GTPBP10</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ADCYAP1\\230237_at</th>\n",
" <td>-1.768758</td>\n",
" <td>-2.173114</td>\n",
" <td>0.033971</td>\n",
" <td>-4.577328</td>\n",
" <td>ADCYAP1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>CRYBA2\\220136_s_at</th>\n",
" <td>0.787749</td>\n",
" <td>2.155419</td>\n",
" <td>0.035394</td>\n",
" <td>-4.577673</td>\n",
" <td>CRYBA2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LMTK2\\235307_at</th>\n",
" <td>-1.246947</td>\n",
" <td>-2.145262</td>\n",
" <td>0.036235</td>\n",
" <td>-4.577870</td>\n",
" <td>LMTK2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PRO2949\\1553374_at</th>\n",
" <td>1.496370</td>\n",
" <td>2.143200</td>\n",
" <td>0.036408</td>\n",
" <td>-4.577910</td>\n",
" <td>PRO2949</td>\n",
" </tr>\n",
" <tr>\n",
" <th>C9orf130\\234429_at</th>\n",
" <td>1.169090</td>\n",
" <td>2.132408</td>\n",
" <td>0.037324</td>\n",
" <td>-4.578118</td>\n",
" <td>C9orf130</td>\n",
" </tr>\n",
" <tr>\n",
" <th>DNM3\\1558502_s_at</th>\n",
" <td>1.823855</td>\n",
" <td>2.131027</td>\n",
" <td>0.037442</td>\n",
" <td>-4.578145</td>\n",
" <td>DNM3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HBQ1\\220807_at</th>\n",
" <td>-0.815548</td>\n",
" <td>-2.116788</td>\n",
" <td>0.038685</td>\n",
" <td>-4.578419</td>\n",
" <td>HBQ1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100131825\\217442_at</th>\n",
" <td>1.476831</td>\n",
" <td>2.112839</td>\n",
" <td>0.039036</td>\n",
" <td>-4.578494</td>\n",
" <td>LOC100131825</td>\n",
" </tr>\n",
" <tr>\n",
" <th>IL17B\\220273_at</th>\n",
" <td>1.360296</td>\n",
" <td>2.111163</td>\n",
" <td>0.039186</td>\n",
" <td>-4.578527</td>\n",
" <td>IL17B</td>\n",
" </tr>\n",
" <tr>\n",
" <th>MAGEB4\\207580_at</th>\n",
" <td>-1.415009</td>\n",
" <td>-2.104162</td>\n",
" <td>0.039817</td>\n",
" <td>-4.578660</td>\n",
" <td>MAGEB4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PEX26\\235098_at</th>\n",
" <td>1.422767</td>\n",
" <td>2.094647</td>\n",
" <td>0.040689</td>\n",
" <td>-4.578842</td>\n",
" <td>PEX26</td>\n",
" </tr>\n",
" <tr>\n",
" <th>POFUT2\\207448_at</th>\n",
" <td>-0.987136</td>\n",
" <td>-2.091314</td>\n",
" <td>0.040998</td>\n",
" <td>-4.578905</td>\n",
" <td>POFUT2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ART1\\1570480_s_at</th>\n",
" <td>-1.162461</td>\n",
" <td>-2.081568</td>\n",
" <td>0.041915</td>\n",
" <td>-4.579091</td>\n",
" <td>ART1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>CIT\\242872_at</th>\n",
" <td>1.527711</td>\n",
" <td>2.080893</td>\n",
" <td>0.041979</td>\n",
" <td>-4.579103</td>\n",
" <td>CIT</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SSX2\\210497_x_at</th>\n",
" <td>-1.218773</td>\n",
" <td>-2.079931</td>\n",
" <td>0.042070</td>\n",
" <td>-4.579122</td>\n",
" <td>SSX2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>C20orf94\\236390_at</th>\n",
" <td>1.607248</td>\n",
" <td>2.070293</td>\n",
" <td>0.042997</td>\n",
" <td>-4.579304</td>\n",
" <td>C20orf94</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SLC17A1\\1560885_x_at</th>\n",
" <td>-1.133660</td>\n",
" <td>-2.066863</td>\n",
" <td>0.043331</td>\n",
" <td>-4.579369</td>\n",
" <td>SLC17A1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PCP4\\205549_at</th>\n",
" <td>-1.410662</td>\n",
" <td>-2.061366</td>\n",
" <td>0.043871</td>\n",
" <td>-4.579472</td>\n",
" <td>PCP4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GOLM1\\1558248_at</th>\n",
" <td>1.361249</td>\n",
" <td>2.046192</td>\n",
" <td>0.045392</td>\n",
" <td>-4.579757</td>\n",
" <td>GOLM1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>RNASE1\\217093_at</th>\n",
" <td>1.136094</td>\n",
" <td>2.037896</td>\n",
" <td>0.046243</td>\n",
" <td>-4.579913</td>\n",
" <td>RNASE1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ZNRD1-AS\\234457_at</th>\n",
" <td>-1.297711</td>\n",
" <td>-2.036670</td>\n",
" <td>0.046369</td>\n",
" <td>-4.579935</td>\n",
" <td>ZNRD1-AS</td>\n",
" </tr>\n",
" <tr>\n",
" <th>METTL6\\1557991_at</th>\n",
" <td>1.328631</td>\n",
" <td>2.034147</td>\n",
" <td>0.046631</td>\n",
" <td>-4.579982</td>\n",
" <td>METTL6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC389634\\1560119_at</th>\n",
" <td>1.716840</td>\n",
" <td>2.032055</td>\n",
" <td>0.046850</td>\n",
" <td>-4.580021</td>\n",
" <td>LOC389634</td>\n",
" </tr>\n",
" <tr>\n",
" <th>IL2\\207849_at</th>\n",
" <td>-1.448060</td>\n",
" <td>-2.030678</td>\n",
" <td>0.046994</td>\n",
" <td>-4.580047</td>\n",
" <td>IL2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PRLR\\211917_s_at</th>\n",
" <td>1.410709</td>\n",
" <td>2.029950</td>\n",
" <td>0.047070</td>\n",
" <td>-4.580061</td>\n",
" <td>PRLR</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GRIK2\\1555375_at</th>\n",
" <td>-1.422374</td>\n",
" <td>-2.029393</td>\n",
" <td>0.047129</td>\n",
" <td>-4.580071</td>\n",
" <td>GRIK2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>RGS20\\210138_at</th>\n",
" <td>1.453221</td>\n",
" <td>2.029172</td>\n",
" <td>0.047152</td>\n",
" <td>-4.580075</td>\n",
" <td>RGS20</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GP5\\211525_s_at</th>\n",
" <td>-1.216566</td>\n",
" <td>-2.027948</td>\n",
" <td>0.047281</td>\n",
" <td>-4.580098</td>\n",
" <td>GP5</td>\n",
" </tr>\n",
" <tr>\n",
" <th>TSC2\\215624_at</th>\n",
" <td>1.636716</td>\n",
" <td>2.024535</td>\n",
" <td>0.047642</td>\n",
" <td>-4.580161</td>\n",
" <td>TSC2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PDE6A\\206623_at</th>\n",
" <td>1.567774</td>\n",
" <td>2.023391</td>\n",
" <td>0.047763</td>\n",
" <td>-4.580183</td>\n",
" <td>PDE6A</td>\n",
" </tr>\n",
" <tr>\n",
" <th>FAM84A\\228459_at</th>\n",
" <td>1.097656</td>\n",
" <td>2.022142</td>\n",
" <td>0.047896</td>\n",
" <td>-4.580206</td>\n",
" <td>FAM84A</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC283868\\1564683_at</th>\n",
" <td>1.313171</td>\n",
" <td>2.021121</td>\n",
" <td>0.048005</td>\n",
" <td>-4.580225</td>\n",
" <td>LOC283868</td>\n",
" </tr>\n",
" <tr>\n",
" <th>BEND6\\1568820_a_at</th>\n",
" <td>-0.943036</td>\n",
" <td>-2.019456</td>\n",
" <td>0.048183</td>\n",
" <td>-4.580256</td>\n",
" <td>BEND6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>C21orf94\\1553519_at</th>\n",
" <td>-1.175958</td>\n",
" <td>-2.016891</td>\n",
" <td>0.048458</td>\n",
" <td>-4.580303</td>\n",
" <td>C21orf94</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ACTL9\\243208_x_at</th>\n",
" <td>1.103029</td>\n",
" <td>2.010967</td>\n",
" <td>0.049099</td>\n",
" <td>-4.580413</td>\n",
" <td>ACTL9</td>\n",
" </tr>\n",
" <tr>\n",
" <th>EFCAB6\\234732_s_at</th>\n",
" <td>1.412526</td>\n",
" <td>2.006627</td>\n",
" <td>0.049574</td>\n",
" <td>-4.580493</td>\n",
" <td>EFCAB6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>KDSR\\222359_x_at</th>\n",
" <td>1.343963</td>\n",
" <td>2.006528</td>\n",
" <td>0.049585</td>\n",
" <td>-4.580495</td>\n",
" <td>KDSR</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100506920\\237659_at</th>\n",
" <td>0.776889</td>\n",
" <td>2.005503</td>\n",
" <td>0.049697</td>\n",
" <td>-4.580514</td>\n",
" <td>LOC100506920</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SHMT1\\231701_s_at</th>\n",
" <td>-1.117987</td>\n",
" <td>-2.004808</td>\n",
" <td>0.049774</td>\n",
" <td>-4.580527</td>\n",
" <td>SHMT1</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" log_fc t p_value b gene_name\n",
"probe \n",
"IL1F8\\224230_at -1.546104 -3.449570 0.001067 -4.548413 IL1F8\n",
"LOC400590\\1560992_at 2.197704 3.434648 0.001117 -4.548785 LOC400590\n",
"ANGEL1\\244685_at -1.178030 -2.807717 0.006833 -4.563804 ANGEL1\n",
"GRK7\\1552929_at 1.679992 2.562875 0.013065 -4.569267 GRK7\n",
"FLJ33996\\237790_at 1.203864 2.546120 0.013639 -4.569630 FLJ33996\n",
"POSTN\\214981_at 2.156220 2.520897 0.014548 -4.570174 POSTN\n",
"LOC100507153\\1568762_at 1.538902 2.507401 0.015056 -4.570464 LOC100507153\n",
"GPR17\\206190_at 1.318751 2.456309 0.017129 -4.571554 GPR17\n",
"TTC39A\\217101_at 1.249650 2.448672 0.017460 -4.571715 TTC39A\n",
"RNF141\\1565546_at 1.546828 2.437364 0.017960 -4.571954 RNF141\n",
"MAF\\1566323_at -1.440637 -2.433496 0.018134 -4.572036 MAF\n",
"DPF3\\235357_at -1.212370 -2.400648 0.019676 -4.572725 DPF3\n",
"METAP1D\\1565755_at 1.510195 2.399407 0.019736 -4.572750 METAP1D\n",
"ZNF780B\\214899_at 1.644326 2.396825 0.019863 -4.572804 ZNF780B\n",
"RUNX1T1\\216831_s_at 2.096988 2.390294 0.020185 -4.572940 RUNX1T1\n",
"GFRA2\\205722_s_at 1.386836 2.371531 0.021139 -4.573330 GFRA2\n",
"LOC100288139\\234426_x_at 1.580194 2.351281 0.022214 -4.573749 LOC100288139\n",
"C2orf14\\224278_at -1.270161 -2.346501 0.022474 -4.573847 C2orf14\n",
"LOXL4\\1570219_at -1.320024 -2.322838 0.023805 -4.574333 LOXL4\n",
"IGHG1\\216892_at -1.353338 -2.304121 0.024907 -4.574714 IGHG1\n",
"PKLR\\210451_at -0.951392 -2.302312 0.025016 -4.574751 PKLR\n",
"TRAF5\\1569861_at -1.419547 -2.296200 0.025387 -4.574875 TRAF5\n",
"DNAH14\\1567861_at 1.368343 2.294568 0.025487 -4.574908 DNAH14\n",
"GRIA3\\230144_at 1.585759 2.250786 0.028300 -4.575791 GRIA3\n",
"SLC38A10\\1563226_at 1.611960 2.246147 0.028613 -4.575883 SLC38A10\n",
"MARCH7\\1557703_at 1.264078 2.235305 0.029358 -4.576100 MARCH7\n",
"NCOA3\\1562439_at 1.279497 2.219504 0.030475 -4.576414 NCOA3\n",
"LOC100287689\\243665_s_at 1.315087 2.217997 0.030583 -4.576444 LOC100287689\n",
"MAGIX\\219965_s_at 1.666859 2.213778 0.030888 -4.576528 MAGIX\n",
"LOC643763\\1558387_at -1.716835 -2.193242 0.032413 -4.576933 LOC643763\n",
"UBR4\\231889_at 1.342234 2.188355 0.032785 -4.577029 UBR4\n",
"GTPBP10\\230684_at 1.667459 2.178850 0.033520 -4.577215 GTPBP10\n",
"ADCYAP1\\230237_at -1.768758 -2.173114 0.033971 -4.577328 ADCYAP1\n",
"CRYBA2\\220136_s_at 0.787749 2.155419 0.035394 -4.577673 CRYBA2\n",
"LMTK2\\235307_at -1.246947 -2.145262 0.036235 -4.577870 LMTK2\n",
"PRO2949\\1553374_at 1.496370 2.143200 0.036408 -4.577910 PRO2949\n",
"C9orf130\\234429_at 1.169090 2.132408 0.037324 -4.578118 C9orf130\n",
"DNM3\\1558502_s_at 1.823855 2.131027 0.037442 -4.578145 DNM3\n",
"HBQ1\\220807_at -0.815548 -2.116788 0.038685 -4.578419 HBQ1\n",
"LOC100131825\\217442_at 1.476831 2.112839 0.039036 -4.578494 LOC100131825\n",
"IL17B\\220273_at 1.360296 2.111163 0.039186 -4.578527 IL17B\n",
"MAGEB4\\207580_at -1.415009 -2.104162 0.039817 -4.578660 MAGEB4\n",
"PEX26\\235098_at 1.422767 2.094647 0.040689 -4.578842 PEX26\n",
"POFUT2\\207448_at -0.987136 -2.091314 0.040998 -4.578905 POFUT2\n",
"ART1\\1570480_s_at -1.162461 -2.081568 0.041915 -4.579091 ART1\n",
"CIT\\242872_at 1.527711 2.080893 0.041979 -4.579103 CIT\n",
"SSX2\\210497_x_at -1.218773 -2.079931 0.042070 -4.579122 SSX2\n",
"C20orf94\\236390_at 1.607248 2.070293 0.042997 -4.579304 C20orf94\n",
"SLC17A1\\1560885_x_at -1.133660 -2.066863 0.043331 -4.579369 SLC17A1\n",
"PCP4\\205549_at -1.410662 -2.061366 0.043871 -4.579472 PCP4\n",
"GOLM1\\1558248_at 1.361249 2.046192 0.045392 -4.579757 GOLM1\n",
"RNASE1\\217093_at 1.136094 2.037896 0.046243 -4.579913 RNASE1\n",
"ZNRD1-AS\\234457_at -1.297711 -2.036670 0.046369 -4.579935 ZNRD1-AS\n",
"METTL6\\1557991_at 1.328631 2.034147 0.046631 -4.579982 METTL6\n",
"LOC389634\\1560119_at 1.716840 2.032055 0.046850 -4.580021 LOC389634\n",
"IL2\\207849_at -1.448060 -2.030678 0.046994 -4.580047 IL2\n",
"PRLR\\211917_s_at 1.410709 2.029950 0.047070 -4.580061 PRLR\n",
"GRIK2\\1555375_at -1.422374 -2.029393 0.047129 -4.580071 GRIK2\n",
"RGS20\\210138_at 1.453221 2.029172 0.047152 -4.580075 RGS20\n",
"GP5\\211525_s_at -1.216566 -2.027948 0.047281 -4.580098 GP5\n",
"TSC2\\215624_at 1.636716 2.024535 0.047642 -4.580161 TSC2\n",
"PDE6A\\206623_at 1.567774 2.023391 0.047763 -4.580183 PDE6A\n",
"FAM84A\\228459_at 1.097656 2.022142 0.047896 -4.580206 FAM84A\n",
"LOC283868\\1564683_at 1.313171 2.021121 0.048005 -4.580225 LOC283868\n",
"BEND6\\1568820_a_at -0.943036 -2.019456 0.048183 -4.580256 BEND6\n",
"C21orf94\\1553519_at -1.175958 -2.016891 0.048458 -4.580303 C21orf94\n",
"ACTL9\\243208_x_at 1.103029 2.010967 0.049099 -4.580413 ACTL9\n",
"EFCAB6\\234732_s_at 1.412526 2.006627 0.049574 -4.580493 EFCAB6\n",
"KDSR\\222359_x_at 1.343963 2.006528 0.049585 -4.580495 KDSR\n",
"LOC100506920\\237659_at 0.776889 2.005503 0.049697 -4.580514 LOC100506920\n",
"SHMT1\\231701_s_at -1.117987 -2.004808 0.049774 -4.580527 SHMT1"
]
},
"execution_count": 58,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"def get_gene_name(probe):\n",
" return probe.split('\\\\')[0]\n",
"\n",
"top_probes['gene_name'] = top_probes.index.map(get_gene_name)\n",
"top_probes"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Map the gene names to Entrez Gene IDs (which are supported by KEGG API).\n",
"The output table shows **top_probes** again, now with mapped gene_id column:"
]
},
{
"cell_type": "code",
"execution_count": 59,
"metadata": {
"collapsed": false,
"scrolled": true
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>log_fc</th>\n",
" <th>t</th>\n",
" <th>p_value</th>\n",
" <th>b</th>\n",
" <th>gene_name</th>\n",
" <th>gene_id</th>\n",
" </tr>\n",
" <tr>\n",
" <th>probe</th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>IL1F8\\224230_at</th>\n",
" <td>-1.546104</td>\n",
" <td>-3.449570</td>\n",
" <td>0.001067</td>\n",
" <td>-4.548413</td>\n",
" <td>IL1F8</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC400590\\1560992_at</th>\n",
" <td>2.197704</td>\n",
" <td>3.434648</td>\n",
" <td>0.001117</td>\n",
" <td>-4.548785</td>\n",
" <td>LOC400590</td>\n",
" <td>400590</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ANGEL1\\244685_at</th>\n",
" <td>-1.178030</td>\n",
" <td>-2.807717</td>\n",
" <td>0.006833</td>\n",
" <td>-4.563804</td>\n",
" <td>ANGEL1</td>\n",
" <td>23357</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GRK7\\1552929_at</th>\n",
" <td>1.679992</td>\n",
" <td>2.562875</td>\n",
" <td>0.013065</td>\n",
" <td>-4.569267</td>\n",
" <td>GRK7</td>\n",
" <td>131890</td>\n",
" </tr>\n",
" <tr>\n",
" <th>FLJ33996\\237790_at</th>\n",
" <td>1.203864</td>\n",
" <td>2.546120</td>\n",
" <td>0.013639</td>\n",
" <td>-4.569630</td>\n",
" <td>FLJ33996</td>\n",
" <td>283401</td>\n",
" </tr>\n",
" <tr>\n",
" <th>POSTN\\214981_at</th>\n",
" <td>2.156220</td>\n",
" <td>2.520897</td>\n",
" <td>0.014548</td>\n",
" <td>-4.570174</td>\n",
" <td>POSTN</td>\n",
" <td>10631</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100507153\\1568762_at</th>\n",
" <td>1.538902</td>\n",
" <td>2.507401</td>\n",
" <td>0.015056</td>\n",
" <td>-4.570464</td>\n",
" <td>LOC100507153</td>\n",
" <td>100507153</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GPR17\\206190_at</th>\n",
" <td>1.318751</td>\n",
" <td>2.456309</td>\n",
" <td>0.017129</td>\n",
" <td>-4.571554</td>\n",
" <td>GPR17</td>\n",
" <td>2840</td>\n",
" </tr>\n",
" <tr>\n",
" <th>TTC39A\\217101_at</th>\n",
" <td>1.249650</td>\n",
" <td>2.448672</td>\n",
" <td>0.017460</td>\n",
" <td>-4.571715</td>\n",
" <td>TTC39A</td>\n",
" <td>22996</td>\n",
" </tr>\n",
" <tr>\n",
" <th>RNF141\\1565546_at</th>\n",
" <td>1.546828</td>\n",
" <td>2.437364</td>\n",
" <td>0.017960</td>\n",
" <td>-4.571954</td>\n",
" <td>RNF141</td>\n",
" <td>50862</td>\n",
" </tr>\n",
" <tr>\n",
" <th>MAF\\1566323_at</th>\n",
" <td>-1.440637</td>\n",
" <td>-2.433496</td>\n",
" <td>0.018134</td>\n",
" <td>-4.572036</td>\n",
" <td>MAF</td>\n",
" <td>4094</td>\n",
" </tr>\n",
" <tr>\n",
" <th>DPF3\\235357_at</th>\n",
" <td>-1.212370</td>\n",
" <td>-2.400648</td>\n",
" <td>0.019676</td>\n",
" <td>-4.572725</td>\n",
" <td>DPF3</td>\n",
" <td>8110</td>\n",
" </tr>\n",
" <tr>\n",
" <th>METAP1D\\1565755_at</th>\n",
" <td>1.510195</td>\n",
" <td>2.399407</td>\n",
" <td>0.019736</td>\n",
" <td>-4.572750</td>\n",
" <td>METAP1D</td>\n",
" <td>254042</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ZNF780B\\214899_at</th>\n",
" <td>1.644326</td>\n",
" <td>2.396825</td>\n",
" <td>0.019863</td>\n",
" <td>-4.572804</td>\n",
" <td>ZNF780B</td>\n",
" <td>163131</td>\n",
" </tr>\n",
" <tr>\n",
" <th>RUNX1T1\\216831_s_at</th>\n",
" <td>2.096988</td>\n",
" <td>2.390294</td>\n",
" <td>0.020185</td>\n",
" <td>-4.572940</td>\n",
" <td>RUNX1T1</td>\n",
" <td>862</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GFRA2\\205722_s_at</th>\n",
" <td>1.386836</td>\n",
" <td>2.371531</td>\n",
" <td>0.021139</td>\n",
" <td>-4.573330</td>\n",
" <td>GFRA2</td>\n",
" <td>2675</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100288139\\234426_x_at</th>\n",
" <td>1.580194</td>\n",
" <td>2.351281</td>\n",
" <td>0.022214</td>\n",
" <td>-4.573749</td>\n",
" <td>LOC100288139</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>C2orf14\\224278_at</th>\n",
" <td>-1.270161</td>\n",
" <td>-2.346501</td>\n",
" <td>0.022474</td>\n",
" <td>-4.573847</td>\n",
" <td>C2orf14</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOXL4\\1570219_at</th>\n",
" <td>-1.320024</td>\n",
" <td>-2.322838</td>\n",
" <td>0.023805</td>\n",
" <td>-4.574333</td>\n",
" <td>LOXL4</td>\n",
" <td>84171</td>\n",
" </tr>\n",
" <tr>\n",
" <th>IGHG1\\216892_at</th>\n",
" <td>-1.353338</td>\n",
" <td>-2.304121</td>\n",
" <td>0.024907</td>\n",
" <td>-4.574714</td>\n",
" <td>IGHG1</td>\n",
" <td>3500</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PKLR\\210451_at</th>\n",
" <td>-0.951392</td>\n",
" <td>-2.302312</td>\n",
" <td>0.025016</td>\n",
" <td>-4.574751</td>\n",
" <td>PKLR</td>\n",
" <td>5313</td>\n",
" </tr>\n",
" <tr>\n",
" <th>TRAF5\\1569861_at</th>\n",
" <td>-1.419547</td>\n",
" <td>-2.296200</td>\n",
" <td>0.025387</td>\n",
" <td>-4.574875</td>\n",
" <td>TRAF5</td>\n",
" <td>7188</td>\n",
" </tr>\n",
" <tr>\n",
" <th>DNAH14\\1567861_at</th>\n",
" <td>1.368343</td>\n",
" <td>2.294568</td>\n",
" <td>0.025487</td>\n",
" <td>-4.574908</td>\n",
" <td>DNAH14</td>\n",
" <td>127602</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GRIA3\\230144_at</th>\n",
" <td>1.585759</td>\n",
" <td>2.250786</td>\n",
" <td>0.028300</td>\n",
" <td>-4.575791</td>\n",
" <td>GRIA3</td>\n",
" <td>2892</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SLC38A10\\1563226_at</th>\n",
" <td>1.611960</td>\n",
" <td>2.246147</td>\n",
" <td>0.028613</td>\n",
" <td>-4.575883</td>\n",
" <td>SLC38A10</td>\n",
" <td>124565</td>\n",
" </tr>\n",
" <tr>\n",
" <th>MARCH7\\1557703_at</th>\n",
" <td>1.264078</td>\n",
" <td>2.235305</td>\n",
" <td>0.029358</td>\n",
" <td>-4.576100</td>\n",
" <td>MARCH7</td>\n",
" <td>64844</td>\n",
" </tr>\n",
" <tr>\n",
" <th>NCOA3\\1562439_at</th>\n",
" <td>1.279497</td>\n",
" <td>2.219504</td>\n",
" <td>0.030475</td>\n",
" <td>-4.576414</td>\n",
" <td>NCOA3</td>\n",
" <td>8202</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100287689\\243665_s_at</th>\n",
" <td>1.315087</td>\n",
" <td>2.217997</td>\n",
" <td>0.030583</td>\n",
" <td>-4.576444</td>\n",
" <td>LOC100287689</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>MAGIX\\219965_s_at</th>\n",
" <td>1.666859</td>\n",
" <td>2.213778</td>\n",
" <td>0.030888</td>\n",
" <td>-4.576528</td>\n",
" <td>MAGIX</td>\n",
" <td>79917</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC643763\\1558387_at</th>\n",
" <td>-1.716835</td>\n",
" <td>-2.193242</td>\n",
" <td>0.032413</td>\n",
" <td>-4.576933</td>\n",
" <td>LOC643763</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>UBR4\\231889_at</th>\n",
" <td>1.342234</td>\n",
" <td>2.188355</td>\n",
" <td>0.032785</td>\n",
" <td>-4.577029</td>\n",
" <td>UBR4</td>\n",
" <td>23352</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GTPBP10\\230684_at</th>\n",
" <td>1.667459</td>\n",
" <td>2.178850</td>\n",
" <td>0.033520</td>\n",
" <td>-4.577215</td>\n",
" <td>GTPBP10</td>\n",
" <td>85865</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ADCYAP1\\230237_at</th>\n",
" <td>-1.768758</td>\n",
" <td>-2.173114</td>\n",
" <td>0.033971</td>\n",
" <td>-4.577328</td>\n",
" <td>ADCYAP1</td>\n",
" <td>116</td>\n",
" </tr>\n",
" <tr>\n",
" <th>CRYBA2\\220136_s_at</th>\n",
" <td>0.787749</td>\n",
" <td>2.155419</td>\n",
" <td>0.035394</td>\n",
" <td>-4.577673</td>\n",
" <td>CRYBA2</td>\n",
" <td>1412</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LMTK2\\235307_at</th>\n",
" <td>-1.246947</td>\n",
" <td>-2.145262</td>\n",
" <td>0.036235</td>\n",
" <td>-4.577870</td>\n",
" <td>LMTK2</td>\n",
" <td>22853</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PRO2949\\1553374_at</th>\n",
" <td>1.496370</td>\n",
" <td>2.143200</td>\n",
" <td>0.036408</td>\n",
" <td>-4.577910</td>\n",
" <td>PRO2949</td>\n",
" <td>55412</td>\n",
" </tr>\n",
" <tr>\n",
" <th>C9orf130\\234429_at</th>\n",
" <td>1.169090</td>\n",
" <td>2.132408</td>\n",
" <td>0.037324</td>\n",
" <td>-4.578118</td>\n",
" <td>C9orf130</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>DNM3\\1558502_s_at</th>\n",
" <td>1.823855</td>\n",
" <td>2.131027</td>\n",
" <td>0.037442</td>\n",
" <td>-4.578145</td>\n",
" <td>DNM3</td>\n",
" <td>26052</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HBQ1\\220807_at</th>\n",
" <td>-0.815548</td>\n",
" <td>-2.116788</td>\n",
" <td>0.038685</td>\n",
" <td>-4.578419</td>\n",
" <td>HBQ1</td>\n",
" <td>3049</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100131825\\217442_at</th>\n",
" <td>1.476831</td>\n",
" <td>2.112839</td>\n",
" <td>0.039036</td>\n",
" <td>-4.578494</td>\n",
" <td>LOC100131825</td>\n",
" <td>100131825</td>\n",
" </tr>\n",
" <tr>\n",
" <th>IL17B\\220273_at</th>\n",
" <td>1.360296</td>\n",
" <td>2.111163</td>\n",
" <td>0.039186</td>\n",
" <td>-4.578527</td>\n",
" <td>IL17B</td>\n",
" <td>27190</td>\n",
" </tr>\n",
" <tr>\n",
" <th>MAGEB4\\207580_at</th>\n",
" <td>-1.415009</td>\n",
" <td>-2.104162</td>\n",
" <td>0.039817</td>\n",
" <td>-4.578660</td>\n",
" <td>MAGEB4</td>\n",
" <td>4115</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PEX26\\235098_at</th>\n",
" <td>1.422767</td>\n",
" <td>2.094647</td>\n",
" <td>0.040689</td>\n",
" <td>-4.578842</td>\n",
" <td>PEX26</td>\n",
" <td>55670</td>\n",
" </tr>\n",
" <tr>\n",
" <th>POFUT2\\207448_at</th>\n",
" <td>-0.987136</td>\n",
" <td>-2.091314</td>\n",
" <td>0.040998</td>\n",
" <td>-4.578905</td>\n",
" <td>POFUT2</td>\n",
" <td>23275</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ART1\\1570480_s_at</th>\n",
" <td>-1.162461</td>\n",
" <td>-2.081568</td>\n",
" <td>0.041915</td>\n",
" <td>-4.579091</td>\n",
" <td>ART1</td>\n",
" <td>417</td>\n",
" </tr>\n",
" <tr>\n",
" <th>CIT\\242872_at</th>\n",
" <td>1.527711</td>\n",
" <td>2.080893</td>\n",
" <td>0.041979</td>\n",
" <td>-4.579103</td>\n",
" <td>CIT</td>\n",
" <td>11113</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SSX2\\210497_x_at</th>\n",
" <td>-1.218773</td>\n",
" <td>-2.079931</td>\n",
" <td>0.042070</td>\n",
" <td>-4.579122</td>\n",
" <td>SSX2</td>\n",
" <td>6757</td>\n",
" </tr>\n",
" <tr>\n",
" <th>C20orf94\\236390_at</th>\n",
" <td>1.607248</td>\n",
" <td>2.070293</td>\n",
" <td>0.042997</td>\n",
" <td>-4.579304</td>\n",
" <td>C20orf94</td>\n",
" <td>128710</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SLC17A1\\1560885_x_at</th>\n",
" <td>-1.133660</td>\n",
" <td>-2.066863</td>\n",
" <td>0.043331</td>\n",
" <td>-4.579369</td>\n",
" <td>SLC17A1</td>\n",
" <td>6568</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PCP4\\205549_at</th>\n",
" <td>-1.410662</td>\n",
" <td>-2.061366</td>\n",
" <td>0.043871</td>\n",
" <td>-4.579472</td>\n",
" <td>PCP4</td>\n",
" <td>5121</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GOLM1\\1558248_at</th>\n",
" <td>1.361249</td>\n",
" <td>2.046192</td>\n",
" <td>0.045392</td>\n",
" <td>-4.579757</td>\n",
" <td>GOLM1</td>\n",
" <td>51280</td>\n",
" </tr>\n",
" <tr>\n",
" <th>RNASE1\\217093_at</th>\n",
" <td>1.136094</td>\n",
" <td>2.037896</td>\n",
" <td>0.046243</td>\n",
" <td>-4.579913</td>\n",
" <td>RNASE1</td>\n",
" <td>6035</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ZNRD1-AS\\234457_at</th>\n",
" <td>-1.297711</td>\n",
" <td>-2.036670</td>\n",
" <td>0.046369</td>\n",
" <td>-4.579935</td>\n",
" <td>ZNRD1-AS</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>METTL6\\1557991_at</th>\n",
" <td>1.328631</td>\n",
" <td>2.034147</td>\n",
" <td>0.046631</td>\n",
" <td>-4.579982</td>\n",
" <td>METTL6</td>\n",
" <td>131965</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC389634\\1560119_at</th>\n",
" <td>1.716840</td>\n",
" <td>2.032055</td>\n",
" <td>0.046850</td>\n",
" <td>-4.580021</td>\n",
" <td>LOC389634</td>\n",
" <td>389634</td>\n",
" </tr>\n",
" <tr>\n",
" <th>IL2\\207849_at</th>\n",
" <td>-1.448060</td>\n",
" <td>-2.030678</td>\n",
" <td>0.046994</td>\n",
" <td>-4.580047</td>\n",
" <td>IL2</td>\n",
" <td>3558</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PRLR\\211917_s_at</th>\n",
" <td>1.410709</td>\n",
" <td>2.029950</td>\n",
" <td>0.047070</td>\n",
" <td>-4.580061</td>\n",
" <td>PRLR</td>\n",
" <td>5618</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GRIK2\\1555375_at</th>\n",
" <td>-1.422374</td>\n",
" <td>-2.029393</td>\n",
" <td>0.047129</td>\n",
" <td>-4.580071</td>\n",
" <td>GRIK2</td>\n",
" <td>2898</td>\n",
" </tr>\n",
" <tr>\n",
" <th>RGS20\\210138_at</th>\n",
" <td>1.453221</td>\n",
" <td>2.029172</td>\n",
" <td>0.047152</td>\n",
" <td>-4.580075</td>\n",
" <td>RGS20</td>\n",
" <td>8601</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GP5\\211525_s_at</th>\n",
" <td>-1.216566</td>\n",
" <td>-2.027948</td>\n",
" <td>0.047281</td>\n",
" <td>-4.580098</td>\n",
" <td>GP5</td>\n",
" <td>2814</td>\n",
" </tr>\n",
" <tr>\n",
" <th>TSC2\\215624_at</th>\n",
" <td>1.636716</td>\n",
" <td>2.024535</td>\n",
" <td>0.047642</td>\n",
" <td>-4.580161</td>\n",
" <td>TSC2</td>\n",
" <td>7249</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PDE6A\\206623_at</th>\n",
" <td>1.567774</td>\n",
" <td>2.023391</td>\n",
" <td>0.047763</td>\n",
" <td>-4.580183</td>\n",
" <td>PDE6A</td>\n",
" <td>5145</td>\n",
" </tr>\n",
" <tr>\n",
" <th>FAM84A\\228459_at</th>\n",
" <td>1.097656</td>\n",
" <td>2.022142</td>\n",
" <td>0.047896</td>\n",
" <td>-4.580206</td>\n",
" <td>FAM84A</td>\n",
" <td>151354</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC283868\\1564683_at</th>\n",
" <td>1.313171</td>\n",
" <td>2.021121</td>\n",
" <td>0.048005</td>\n",
" <td>-4.580225</td>\n",
" <td>LOC283868</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>BEND6\\1568820_a_at</th>\n",
" <td>-0.943036</td>\n",
" <td>-2.019456</td>\n",
" <td>0.048183</td>\n",
" <td>-4.580256</td>\n",
" <td>BEND6</td>\n",
" <td>221336</td>\n",
" </tr>\n",
" <tr>\n",
" <th>C21orf94\\1553519_at</th>\n",
" <td>-1.175958</td>\n",
" <td>-2.016891</td>\n",
" <td>0.048458</td>\n",
" <td>-4.580303</td>\n",
" <td>C21orf94</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ACTL9\\243208_x_at</th>\n",
" <td>1.103029</td>\n",
" <td>2.010967</td>\n",
" <td>0.049099</td>\n",
" <td>-4.580413</td>\n",
" <td>ACTL9</td>\n",
" <td>284382</td>\n",
" </tr>\n",
" <tr>\n",
" <th>EFCAB6\\234732_s_at</th>\n",
" <td>1.412526</td>\n",
" <td>2.006627</td>\n",
" <td>0.049574</td>\n",
" <td>-4.580493</td>\n",
" <td>EFCAB6</td>\n",
" <td>64800</td>\n",
" </tr>\n",
" <tr>\n",
" <th>KDSR\\222359_x_at</th>\n",
" <td>1.343963</td>\n",
" <td>2.006528</td>\n",
" <td>0.049585</td>\n",
" <td>-4.580495</td>\n",
" <td>KDSR</td>\n",
" <td>2531</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100506920\\237659_at</th>\n",
" <td>0.776889</td>\n",
" <td>2.005503</td>\n",
" <td>0.049697</td>\n",
" <td>-4.580514</td>\n",
" <td>LOC100506920</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SHMT1\\231701_s_at</th>\n",
" <td>-1.117987</td>\n",
" <td>-2.004808</td>\n",
" <td>0.049774</td>\n",
" <td>-4.580527</td>\n",
" <td>SHMT1</td>\n",
" <td>6470</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" log_fc t p_value b \\\n",
"probe \n",
"IL1F8\\224230_at -1.546104 -3.449570 0.001067 -4.548413 \n",
"LOC400590\\1560992_at 2.197704 3.434648 0.001117 -4.548785 \n",
"ANGEL1\\244685_at -1.178030 -2.807717 0.006833 -4.563804 \n",
"GRK7\\1552929_at 1.679992 2.562875 0.013065 -4.569267 \n",
"FLJ33996\\237790_at 1.203864 2.546120 0.013639 -4.569630 \n",
"POSTN\\214981_at 2.156220 2.520897 0.014548 -4.570174 \n",
"LOC100507153\\1568762_at 1.538902 2.507401 0.015056 -4.570464 \n",
"GPR17\\206190_at 1.318751 2.456309 0.017129 -4.571554 \n",
"TTC39A\\217101_at 1.249650 2.448672 0.017460 -4.571715 \n",
"RNF141\\1565546_at 1.546828 2.437364 0.017960 -4.571954 \n",
"MAF\\1566323_at -1.440637 -2.433496 0.018134 -4.572036 \n",
"DPF3\\235357_at -1.212370 -2.400648 0.019676 -4.572725 \n",
"METAP1D\\1565755_at 1.510195 2.399407 0.019736 -4.572750 \n",
"ZNF780B\\214899_at 1.644326 2.396825 0.019863 -4.572804 \n",
"RUNX1T1\\216831_s_at 2.096988 2.390294 0.020185 -4.572940 \n",
"GFRA2\\205722_s_at 1.386836 2.371531 0.021139 -4.573330 \n",
"LOC100288139\\234426_x_at 1.580194 2.351281 0.022214 -4.573749 \n",
"C2orf14\\224278_at -1.270161 -2.346501 0.022474 -4.573847 \n",
"LOXL4\\1570219_at -1.320024 -2.322838 0.023805 -4.574333 \n",
"IGHG1\\216892_at -1.353338 -2.304121 0.024907 -4.574714 \n",
"PKLR\\210451_at -0.951392 -2.302312 0.025016 -4.574751 \n",
"TRAF5\\1569861_at -1.419547 -2.296200 0.025387 -4.574875 \n",
"DNAH14\\1567861_at 1.368343 2.294568 0.025487 -4.574908 \n",
"GRIA3\\230144_at 1.585759 2.250786 0.028300 -4.575791 \n",
"SLC38A10\\1563226_at 1.611960 2.246147 0.028613 -4.575883 \n",
"MARCH7\\1557703_at 1.264078 2.235305 0.029358 -4.576100 \n",
"NCOA3\\1562439_at 1.279497 2.219504 0.030475 -4.576414 \n",
"LOC100287689\\243665_s_at 1.315087 2.217997 0.030583 -4.576444 \n",
"MAGIX\\219965_s_at 1.666859 2.213778 0.030888 -4.576528 \n",
"LOC643763\\1558387_at -1.716835 -2.193242 0.032413 -4.576933 \n",
"UBR4\\231889_at 1.342234 2.188355 0.032785 -4.577029 \n",
"GTPBP10\\230684_at 1.667459 2.178850 0.033520 -4.577215 \n",
"ADCYAP1\\230237_at -1.768758 -2.173114 0.033971 -4.577328 \n",
"CRYBA2\\220136_s_at 0.787749 2.155419 0.035394 -4.577673 \n",
"LMTK2\\235307_at -1.246947 -2.145262 0.036235 -4.577870 \n",
"PRO2949\\1553374_at 1.496370 2.143200 0.036408 -4.577910 \n",
"C9orf130\\234429_at 1.169090 2.132408 0.037324 -4.578118 \n",
"DNM3\\1558502_s_at 1.823855 2.131027 0.037442 -4.578145 \n",
"HBQ1\\220807_at -0.815548 -2.116788 0.038685 -4.578419 \n",
"LOC100131825\\217442_at 1.476831 2.112839 0.039036 -4.578494 \n",
"IL17B\\220273_at 1.360296 2.111163 0.039186 -4.578527 \n",
"MAGEB4\\207580_at -1.415009 -2.104162 0.039817 -4.578660 \n",
"PEX26\\235098_at 1.422767 2.094647 0.040689 -4.578842 \n",
"POFUT2\\207448_at -0.987136 -2.091314 0.040998 -4.578905 \n",
"ART1\\1570480_s_at -1.162461 -2.081568 0.041915 -4.579091 \n",
"CIT\\242872_at 1.527711 2.080893 0.041979 -4.579103 \n",
"SSX2\\210497_x_at -1.218773 -2.079931 0.042070 -4.579122 \n",
"C20orf94\\236390_at 1.607248 2.070293 0.042997 -4.579304 \n",
"SLC17A1\\1560885_x_at -1.133660 -2.066863 0.043331 -4.579369 \n",
"PCP4\\205549_at -1.410662 -2.061366 0.043871 -4.579472 \n",
"GOLM1\\1558248_at 1.361249 2.046192 0.045392 -4.579757 \n",
"RNASE1\\217093_at 1.136094 2.037896 0.046243 -4.579913 \n",
"ZNRD1-AS\\234457_at -1.297711 -2.036670 0.046369 -4.579935 \n",
"METTL6\\1557991_at 1.328631 2.034147 0.046631 -4.579982 \n",
"LOC389634\\1560119_at 1.716840 2.032055 0.046850 -4.580021 \n",
"IL2\\207849_at -1.448060 -2.030678 0.046994 -4.580047 \n",
"PRLR\\211917_s_at 1.410709 2.029950 0.047070 -4.580061 \n",
"GRIK2\\1555375_at -1.422374 -2.029393 0.047129 -4.580071 \n",
"RGS20\\210138_at 1.453221 2.029172 0.047152 -4.580075 \n",
"GP5\\211525_s_at -1.216566 -2.027948 0.047281 -4.580098 \n",
"TSC2\\215624_at 1.636716 2.024535 0.047642 -4.580161 \n",
"PDE6A\\206623_at 1.567774 2.023391 0.047763 -4.580183 \n",
"FAM84A\\228459_at 1.097656 2.022142 0.047896 -4.580206 \n",
"LOC283868\\1564683_at 1.313171 2.021121 0.048005 -4.580225 \n",
"BEND6\\1568820_a_at -0.943036 -2.019456 0.048183 -4.580256 \n",
"C21orf94\\1553519_at -1.175958 -2.016891 0.048458 -4.580303 \n",
"ACTL9\\243208_x_at 1.103029 2.010967 0.049099 -4.580413 \n",
"EFCAB6\\234732_s_at 1.412526 2.006627 0.049574 -4.580493 \n",
"KDSR\\222359_x_at 1.343963 2.006528 0.049585 -4.580495 \n",
"LOC100506920\\237659_at 0.776889 2.005503 0.049697 -4.580514 \n",
"SHMT1\\231701_s_at -1.117987 -2.004808 0.049774 -4.580527 \n",
"\n",
" gene_name gene_id \n",
"probe \n",
"IL1F8\\224230_at IL1F8 None \n",
"LOC400590\\1560992_at LOC400590 400590 \n",
"ANGEL1\\244685_at ANGEL1 23357 \n",
"GRK7\\1552929_at GRK7 131890 \n",
"FLJ33996\\237790_at FLJ33996 283401 \n",
"POSTN\\214981_at POSTN 10631 \n",
"LOC100507153\\1568762_at LOC100507153 100507153 \n",
"GPR17\\206190_at GPR17 2840 \n",
"TTC39A\\217101_at TTC39A 22996 \n",
"RNF141\\1565546_at RNF141 50862 \n",
"MAF\\1566323_at MAF 4094 \n",
"DPF3\\235357_at DPF3 8110 \n",
"METAP1D\\1565755_at METAP1D 254042 \n",
"ZNF780B\\214899_at ZNF780B 163131 \n",
"RUNX1T1\\216831_s_at RUNX1T1 862 \n",
"GFRA2\\205722_s_at GFRA2 2675 \n",
"LOC100288139\\234426_x_at LOC100288139 None \n",
"C2orf14\\224278_at C2orf14 None \n",
"LOXL4\\1570219_at LOXL4 84171 \n",
"IGHG1\\216892_at IGHG1 3500 \n",
"PKLR\\210451_at PKLR 5313 \n",
"TRAF5\\1569861_at TRAF5 7188 \n",
"DNAH14\\1567861_at DNAH14 127602 \n",
"GRIA3\\230144_at GRIA3 2892 \n",
"SLC38A10\\1563226_at SLC38A10 124565 \n",
"MARCH7\\1557703_at MARCH7 64844 \n",
"NCOA3\\1562439_at NCOA3 8202 \n",
"LOC100287689\\243665_s_at LOC100287689 None \n",
"MAGIX\\219965_s_at MAGIX 79917 \n",
"LOC643763\\1558387_at LOC643763 None \n",
"UBR4\\231889_at UBR4 23352 \n",
"GTPBP10\\230684_at GTPBP10 85865 \n",
"ADCYAP1\\230237_at ADCYAP1 116 \n",
"CRYBA2\\220136_s_at CRYBA2 1412 \n",
"LMTK2\\235307_at LMTK2 22853 \n",
"PRO2949\\1553374_at PRO2949 55412 \n",
"C9orf130\\234429_at C9orf130 None \n",
"DNM3\\1558502_s_at DNM3 26052 \n",
"HBQ1\\220807_at HBQ1 3049 \n",
"LOC100131825\\217442_at LOC100131825 100131825 \n",
"IL17B\\220273_at IL17B 27190 \n",
"MAGEB4\\207580_at MAGEB4 4115 \n",
"PEX26\\235098_at PEX26 55670 \n",
"POFUT2\\207448_at POFUT2 23275 \n",
"ART1\\1570480_s_at ART1 417 \n",
"CIT\\242872_at CIT 11113 \n",
"SSX2\\210497_x_at SSX2 6757 \n",
"C20orf94\\236390_at C20orf94 128710 \n",
"SLC17A1\\1560885_x_at SLC17A1 6568 \n",
"PCP4\\205549_at PCP4 5121 \n",
"GOLM1\\1558248_at GOLM1 51280 \n",
"RNASE1\\217093_at RNASE1 6035 \n",
"ZNRD1-AS\\234457_at ZNRD1-AS None \n",
"METTL6\\1557991_at METTL6 131965 \n",
"LOC389634\\1560119_at LOC389634 389634 \n",
"IL2\\207849_at IL2 3558 \n",
"PRLR\\211917_s_at PRLR 5618 \n",
"GRIK2\\1555375_at GRIK2 2898 \n",
"RGS20\\210138_at RGS20 8601 \n",
"GP5\\211525_s_at GP5 2814 \n",
"TSC2\\215624_at TSC2 7249 \n",
"PDE6A\\206623_at PDE6A 5145 \n",
"FAM84A\\228459_at FAM84A 151354 \n",
"LOC283868\\1564683_at LOC283868 None \n",
"BEND6\\1568820_a_at BEND6 221336 \n",
"C21orf94\\1553519_at C21orf94 None \n",
"ACTL9\\243208_x_at ACTL9 284382 \n",
"EFCAB6\\234732_s_at EFCAB6 64800 \n",
"KDSR\\222359_x_at KDSR 2531 \n",
"LOC100506920\\237659_at LOC100506920 None \n",
"SHMT1\\231701_s_at SHMT1 6470 "
]
},
"execution_count": 59,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from utils import Entrez\n",
"\n",
"entrez = Entrez()\n",
"\n",
"top_probes['gene_id'] = top_probes.gene_name.map(entrez.get_gene_id)\n",
"top_probes"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Search via the KEGG API\n",
"Here we use our custom Python class **Kegg** which calls the KEGG API to find the pathways in KEGG that match one or more of the gene_ids. The output table displays the **top_probes** again, now with a column containing the pathway(s) in which this gene is found. The pathway names are also links to their corresponding entry in the KEGG website.\n",
"We expect some genes to be found in one pathway, some genes in many pathways and many genes in none of the pathways."
]
},
{
"cell_type": "code",
"execution_count": 60,
"metadata": {
"collapsed": false,
"scrolled": true
},
"outputs": [
{
"data": {
"text/html": [
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>log_fc</th>\n",
" <th>t</th>\n",
" <th>p_value</th>\n",
" <th>b</th>\n",
" <th>gene_name</th>\n",
" <th>gene_id</th>\n",
" <th>pathways_ids</th>\n",
" </tr>\n",
" <tr>\n",
" <th>probe</th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>IL1F8\\224230_at</th>\n",
" <td>-1.546104</td>\n",
" <td>-3.449570</td>\n",
" <td>0.001067</td>\n",
" <td>-4.548413</td>\n",
" <td>IL1F8</td>\n",
" <td>None</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC400590\\1560992_at</th>\n",
" <td>2.197704</td>\n",
" <td>3.434648</td>\n",
" <td>0.001117</td>\n",
" <td>-4.548785</td>\n",
" <td>LOC400590</td>\n",
" <td>400590</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ANGEL1\\244685_at</th>\n",
" <td>-1.178030</td>\n",
" <td>-2.807717</td>\n",
" <td>0.006833</td>\n",
" <td>-4.563804</td>\n",
" <td>ANGEL1</td>\n",
" <td>23357</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GRK7\\1552929_at</th>\n",
" <td>1.679992</td>\n",
" <td>2.562875</td>\n",
" <td>0.013065</td>\n",
" <td>-4.569267</td>\n",
" <td>GRK7</td>\n",
" <td>131890</td>\n",
" <td>[<a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04062+131890\">hsa04062</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04144+131890\">hsa04144</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04744+131890\">hsa04744</a>]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>FLJ33996\\237790_at</th>\n",
" <td>1.203864</td>\n",
" <td>2.546120</td>\n",
" <td>0.013639</td>\n",
" <td>-4.569630</td>\n",
" <td>FLJ33996</td>\n",
" <td>283401</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>POSTN\\214981_at</th>\n",
" <td>2.156220</td>\n",
" <td>2.520897</td>\n",
" <td>0.014548</td>\n",
" <td>-4.570174</td>\n",
" <td>POSTN</td>\n",
" <td>10631</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100507153\\1568762_at</th>\n",
" <td>1.538902</td>\n",
" <td>2.507401</td>\n",
" <td>0.015056</td>\n",
" <td>-4.570464</td>\n",
" <td>LOC100507153</td>\n",
" <td>100507153</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GPR17\\206190_at</th>\n",
" <td>1.318751</td>\n",
" <td>2.456309</td>\n",
" <td>0.017129</td>\n",
" <td>-4.571554</td>\n",
" <td>GPR17</td>\n",
" <td>2840</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>TTC39A\\217101_at</th>\n",
" <td>1.249650</td>\n",
" <td>2.448672</td>\n",
" <td>0.017460</td>\n",
" <td>-4.571715</td>\n",
" <td>TTC39A</td>\n",
" <td>22996</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>RNF141\\1565546_at</th>\n",
" <td>1.546828</td>\n",
" <td>2.437364</td>\n",
" <td>0.017960</td>\n",
" <td>-4.571954</td>\n",
" <td>RNF141</td>\n",
" <td>50862</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>MAF\\1566323_at</th>\n",
" <td>-1.440637</td>\n",
" <td>-2.433496</td>\n",
" <td>0.018134</td>\n",
" <td>-4.572036</td>\n",
" <td>MAF</td>\n",
" <td>4094</td>\n",
" <td>[<a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05202+4094\">hsa05202</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05321+4094\">hsa05321</a>]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>DPF3\\235357_at</th>\n",
" <td>-1.212370</td>\n",
" <td>-2.400648</td>\n",
" <td>0.019676</td>\n",
" <td>-4.572725</td>\n",
" <td>DPF3</td>\n",
" <td>8110</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>METAP1D\\1565755_at</th>\n",
" <td>1.510195</td>\n",
" <td>2.399407</td>\n",
" <td>0.019736</td>\n",
" <td>-4.572750</td>\n",
" <td>METAP1D</td>\n",
" <td>254042</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ZNF780B\\214899_at</th>\n",
" <td>1.644326</td>\n",
" <td>2.396825</td>\n",
" <td>0.019863</td>\n",
" <td>-4.572804</td>\n",
" <td>ZNF780B</td>\n",
" <td>163131</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>RUNX1T1\\216831_s_at</th>\n",
" <td>2.096988</td>\n",
" <td>2.390294</td>\n",
" <td>0.020185</td>\n",
" <td>-4.572940</td>\n",
" <td>RUNX1T1</td>\n",
" <td>862</td>\n",
" <td>[<a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05200+862\">hsa05200</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05202+862\">hsa05202</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05221+862\">hsa05221</a>]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GFRA2\\205722_s_at</th>\n",
" <td>1.386836</td>\n",
" <td>2.371531</td>\n",
" <td>0.021139</td>\n",
" <td>-4.573330</td>\n",
" <td>GFRA2</td>\n",
" <td>2675</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100288139\\234426_x_at</th>\n",
" <td>1.580194</td>\n",
" <td>2.351281</td>\n",
" <td>0.022214</td>\n",
" <td>-4.573749</td>\n",
" <td>LOC100288139</td>\n",
" <td>None</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>C2orf14\\224278_at</th>\n",
" <td>-1.270161</td>\n",
" <td>-2.346501</td>\n",
" <td>0.022474</td>\n",
" <td>-4.573847</td>\n",
" <td>C2orf14</td>\n",
" <td>None</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOXL4\\1570219_at</th>\n",
" <td>-1.320024</td>\n",
" <td>-2.322838</td>\n",
" <td>0.023805</td>\n",
" <td>-4.574333</td>\n",
" <td>LOXL4</td>\n",
" <td>84171</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>IGHG1\\216892_at</th>\n",
" <td>-1.353338</td>\n",
" <td>-2.304121</td>\n",
" <td>0.024907</td>\n",
" <td>-4.574714</td>\n",
" <td>IGHG1</td>\n",
" <td>3500</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PKLR\\210451_at</th>\n",
" <td>-0.951392</td>\n",
" <td>-2.302312</td>\n",
" <td>0.025016</td>\n",
" <td>-4.574751</td>\n",
" <td>PKLR</td>\n",
" <td>5313</td>\n",
" <td>[<a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa00010+5313\">hsa00010</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa00230+5313\">hsa00230</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa00620+5313\">hsa00620</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa01100+5313\">hsa01100</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa01130+5313\">hsa01130</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa01200+5313\">hsa01200</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa01230+5313\">hsa01230</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04910+5313\">hsa04910</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04930+5313\">hsa04930</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04932+5313\">hsa04932</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04950+5313\">hsa04950</a>]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>TRAF5\\1569861_at</th>\n",
" <td>-1.419547</td>\n",
" <td>-2.296200</td>\n",
" <td>0.025387</td>\n",
" <td>-4.574875</td>\n",
" <td>TRAF5</td>\n",
" <td>7188</td>\n",
" <td>[<a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04064+7188\">hsa04064</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04668+7188\">hsa04668</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05168+7188\">hsa05168</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05169+7188\">hsa05169</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05200+7188\">hsa05200</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05203+7188\">hsa05203</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05222+7188\">hsa05222</a>]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>DNAH14\\1567861_at</th>\n",
" <td>1.368343</td>\n",
" <td>2.294568</td>\n",
" <td>0.025487</td>\n",
" <td>-4.574908</td>\n",
" <td>DNAH14</td>\n",
" <td>127602</td>\n",
" <td>[<a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05016+127602\">hsa05016</a>]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GRIA3\\230144_at</th>\n",
" <td>1.585759</td>\n",
" <td>2.250786</td>\n",
" <td>0.028300</td>\n",
" <td>-4.575791</td>\n",
" <td>GRIA3</td>\n",
" <td>2892</td>\n",
" <td>[<a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04024+2892\">hsa04024</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04080+2892\">hsa04080</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04713+2892\">hsa04713</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04723+2892\">hsa04723</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04724+2892\">hsa04724</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04728+2892\">hsa04728</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04730+2892\">hsa04730</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05031+2892\">hsa05031</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05033+2892\">hsa05033</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05202+2892\">hsa05202</a>]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SLC38A10\\1563226_at</th>\n",
" <td>1.611960</td>\n",
" <td>2.246147</td>\n",
" <td>0.028613</td>\n",
" <td>-4.575883</td>\n",
" <td>SLC38A10</td>\n",
" <td>124565</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>MARCH7\\1557703_at</th>\n",
" <td>1.264078</td>\n",
" <td>2.235305</td>\n",
" <td>0.029358</td>\n",
" <td>-4.576100</td>\n",
" <td>MARCH7</td>\n",
" <td>64844</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>NCOA3\\1562439_at</th>\n",
" <td>1.279497</td>\n",
" <td>2.219504</td>\n",
" <td>0.030475</td>\n",
" <td>-4.576414</td>\n",
" <td>NCOA3</td>\n",
" <td>8202</td>\n",
" <td>[<a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04919+8202\">hsa04919</a>]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100287689\\243665_s_at</th>\n",
" <td>1.315087</td>\n",
" <td>2.217997</td>\n",
" <td>0.030583</td>\n",
" <td>-4.576444</td>\n",
" <td>LOC100287689</td>\n",
" <td>None</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>MAGIX\\219965_s_at</th>\n",
" <td>1.666859</td>\n",
" <td>2.213778</td>\n",
" <td>0.030888</td>\n",
" <td>-4.576528</td>\n",
" <td>MAGIX</td>\n",
" <td>79917</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC643763\\1558387_at</th>\n",
" <td>-1.716835</td>\n",
" <td>-2.193242</td>\n",
" <td>0.032413</td>\n",
" <td>-4.576933</td>\n",
" <td>LOC643763</td>\n",
" <td>None</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>UBR4\\231889_at</th>\n",
" <td>1.342234</td>\n",
" <td>2.188355</td>\n",
" <td>0.032785</td>\n",
" <td>-4.577029</td>\n",
" <td>UBR4</td>\n",
" <td>23352</td>\n",
" <td>[<a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05203+23352\">hsa05203</a>]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GTPBP10\\230684_at</th>\n",
" <td>1.667459</td>\n",
" <td>2.178850</td>\n",
" <td>0.033520</td>\n",
" <td>-4.577215</td>\n",
" <td>GTPBP10</td>\n",
" <td>85865</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ADCYAP1\\230237_at</th>\n",
" <td>-1.768758</td>\n",
" <td>-2.173114</td>\n",
" <td>0.033971</td>\n",
" <td>-4.577328</td>\n",
" <td>ADCYAP1</td>\n",
" <td>116</td>\n",
" <td>[<a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04911+116\">hsa04911</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04924+116\">hsa04924</a>]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>CRYBA2\\220136_s_at</th>\n",
" <td>0.787749</td>\n",
" <td>2.155419</td>\n",
" <td>0.035394</td>\n",
" <td>-4.577673</td>\n",
" <td>CRYBA2</td>\n",
" <td>1412</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LMTK2\\235307_at</th>\n",
" <td>-1.246947</td>\n",
" <td>-2.145262</td>\n",
" <td>0.036235</td>\n",
" <td>-4.577870</td>\n",
" <td>LMTK2</td>\n",
" <td>22853</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PRO2949\\1553374_at</th>\n",
" <td>1.496370</td>\n",
" <td>2.143200</td>\n",
" <td>0.036408</td>\n",
" <td>-4.577910</td>\n",
" <td>PRO2949</td>\n",
" <td>55412</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>C9orf130\\234429_at</th>\n",
" <td>1.169090</td>\n",
" <td>2.132408</td>\n",
" <td>0.037324</td>\n",
" <td>-4.578118</td>\n",
" <td>C9orf130</td>\n",
" <td>None</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>DNM3\\1558502_s_at</th>\n",
" <td>1.823855</td>\n",
" <td>2.131027</td>\n",
" <td>0.037442</td>\n",
" <td>-4.578145</td>\n",
" <td>DNM3</td>\n",
" <td>26052</td>\n",
" <td>[<a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04144+26052\">hsa04144</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04721+26052\">hsa04721</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04961+26052\">hsa04961</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05100+26052\">hsa05100</a>]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HBQ1\\220807_at</th>\n",
" <td>-0.815548</td>\n",
" <td>-2.116788</td>\n",
" <td>0.038685</td>\n",
" <td>-4.578419</td>\n",
" <td>HBQ1</td>\n",
" <td>3049</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100131825\\217442_at</th>\n",
" <td>1.476831</td>\n",
" <td>2.112839</td>\n",
" <td>0.039036</td>\n",
" <td>-4.578494</td>\n",
" <td>LOC100131825</td>\n",
" <td>100131825</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>IL17B\\220273_at</th>\n",
" <td>1.360296</td>\n",
" <td>2.111163</td>\n",
" <td>0.039186</td>\n",
" <td>-4.578527</td>\n",
" <td>IL17B</td>\n",
" <td>27190</td>\n",
" <td>[<a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04060+27190\">hsa04060</a>]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>MAGEB4\\207580_at</th>\n",
" <td>-1.415009</td>\n",
" <td>-2.104162</td>\n",
" <td>0.039817</td>\n",
" <td>-4.578660</td>\n",
" <td>MAGEB4</td>\n",
" <td>4115</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PEX26\\235098_at</th>\n",
" <td>1.422767</td>\n",
" <td>2.094647</td>\n",
" <td>0.040689</td>\n",
" <td>-4.578842</td>\n",
" <td>PEX26</td>\n",
" <td>55670</td>\n",
" <td>[<a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04146+55670\">hsa04146</a>]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>POFUT2\\207448_at</th>\n",
" <td>-0.987136</td>\n",
" <td>-2.091314</td>\n",
" <td>0.040998</td>\n",
" <td>-4.578905</td>\n",
" <td>POFUT2</td>\n",
" <td>23275</td>\n",
" <td>[<a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa00514+23275\">hsa00514</a>]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ART1\\1570480_s_at</th>\n",
" <td>-1.162461</td>\n",
" <td>-2.081568</td>\n",
" <td>0.041915</td>\n",
" <td>-4.579091</td>\n",
" <td>ART1</td>\n",
" <td>417</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>CIT\\242872_at</th>\n",
" <td>1.527711</td>\n",
" <td>2.080893</td>\n",
" <td>0.041979</td>\n",
" <td>-4.579103</td>\n",
" <td>CIT</td>\n",
" <td>11113</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SSX2\\210497_x_at</th>\n",
" <td>-1.218773</td>\n",
" <td>-2.079931</td>\n",
" <td>0.042070</td>\n",
" <td>-4.579122</td>\n",
" <td>SSX2</td>\n",
" <td>6757</td>\n",
" <td>[<a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05202+6757\">hsa05202</a>]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>C20orf94\\236390_at</th>\n",
" <td>1.607248</td>\n",
" <td>2.070293</td>\n",
" <td>0.042997</td>\n",
" <td>-4.579304</td>\n",
" <td>C20orf94</td>\n",
" <td>128710</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SLC17A1\\1560885_x_at</th>\n",
" <td>-1.133660</td>\n",
" <td>-2.066863</td>\n",
" <td>0.043331</td>\n",
" <td>-4.579369</td>\n",
" <td>SLC17A1</td>\n",
" <td>6568</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PCP4\\205549_at</th>\n",
" <td>-1.410662</td>\n",
" <td>-2.061366</td>\n",
" <td>0.043871</td>\n",
" <td>-4.579472</td>\n",
" <td>PCP4</td>\n",
" <td>5121</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GOLM1\\1558248_at</th>\n",
" <td>1.361249</td>\n",
" <td>2.046192</td>\n",
" <td>0.045392</td>\n",
" <td>-4.579757</td>\n",
" <td>GOLM1</td>\n",
" <td>51280</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>RNASE1\\217093_at</th>\n",
" <td>1.136094</td>\n",
" <td>2.037896</td>\n",
" <td>0.046243</td>\n",
" <td>-4.579913</td>\n",
" <td>RNASE1</td>\n",
" <td>6035</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ZNRD1-AS\\234457_at</th>\n",
" <td>-1.297711</td>\n",
" <td>-2.036670</td>\n",
" <td>0.046369</td>\n",
" <td>-4.579935</td>\n",
" <td>ZNRD1-AS</td>\n",
" <td>None</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>METTL6\\1557991_at</th>\n",
" <td>1.328631</td>\n",
" <td>2.034147</td>\n",
" <td>0.046631</td>\n",
" <td>-4.579982</td>\n",
" <td>METTL6</td>\n",
" <td>131965</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC389634\\1560119_at</th>\n",
" <td>1.716840</td>\n",
" <td>2.032055</td>\n",
" <td>0.046850</td>\n",
" <td>-4.580021</td>\n",
" <td>LOC389634</td>\n",
" <td>389634</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>IL2\\207849_at</th>\n",
" <td>-1.448060</td>\n",
" <td>-2.030678</td>\n",
" <td>0.046994</td>\n",
" <td>-4.580047</td>\n",
" <td>IL2</td>\n",
" <td>3558</td>\n",
" <td>[<a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04060+3558\">hsa04060</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04151+3558\">hsa04151</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04630+3558\">hsa04630</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04660+3558\">hsa04660</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04672+3558\">hsa04672</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04940+3558\">hsa04940</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05142+3558\">hsa05142</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05162+3558\">hsa05162</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05166+3558\">hsa05166</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05320+3558\">hsa05320</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05321+3558\">hsa05321</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05330+3558\">hsa05330</a>, <a target=\"_blank\" href...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PRLR\\211917_s_at</th>\n",
" <td>1.410709</td>\n",
" <td>2.029950</td>\n",
" <td>0.047070</td>\n",
" <td>-4.580061</td>\n",
" <td>PRLR</td>\n",
" <td>5618</td>\n",
" <td>[<a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04060+5618\">hsa04060</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04080+5618\">hsa04080</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04151+5618\">hsa04151</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04630+5618\">hsa04630</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04917+5618\">hsa04917</a>]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GRIK2\\1555375_at</th>\n",
" <td>-1.422374</td>\n",
" <td>-2.029393</td>\n",
" <td>0.047129</td>\n",
" <td>-4.580071</td>\n",
" <td>GRIK2</td>\n",
" <td>2898</td>\n",
" <td>[<a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04080+2898\">hsa04080</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04724+2898\">hsa04724</a>]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>RGS20\\210138_at</th>\n",
" <td>1.453221</td>\n",
" <td>2.029172</td>\n",
" <td>0.047152</td>\n",
" <td>-4.580075</td>\n",
" <td>RGS20</td>\n",
" <td>8601</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>GP5\\211525_s_at</th>\n",
" <td>-1.216566</td>\n",
" <td>-2.027948</td>\n",
" <td>0.047281</td>\n",
" <td>-4.580098</td>\n",
" <td>GP5</td>\n",
" <td>2814</td>\n",
" <td>[<a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04512+2814\">hsa04512</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04611+2814\">hsa04611</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04640+2814\">hsa04640</a>]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>TSC2\\215624_at</th>\n",
" <td>1.636716</td>\n",
" <td>2.024535</td>\n",
" <td>0.047642</td>\n",
" <td>-4.580161</td>\n",
" <td>TSC2</td>\n",
" <td>7249</td>\n",
" <td>[<a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04115+7249\">hsa04115</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04150+7249\">hsa04150</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04151+7249\">hsa04151</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04152+7249\">hsa04152</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04910+7249\">hsa04910</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04919+7249\">hsa04919</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05231+7249\">hsa05231</a>]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>PDE6A\\206623_at</th>\n",
" <td>1.567774</td>\n",
" <td>2.023391</td>\n",
" <td>0.047763</td>\n",
" <td>-4.580183</td>\n",
" <td>PDE6A</td>\n",
" <td>5145</td>\n",
" <td>[<a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa00230+5145\">hsa00230</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04744+5145\">hsa04744</a>]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>FAM84A\\228459_at</th>\n",
" <td>1.097656</td>\n",
" <td>2.022142</td>\n",
" <td>0.047896</td>\n",
" <td>-4.580206</td>\n",
" <td>FAM84A</td>\n",
" <td>151354</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC283868\\1564683_at</th>\n",
" <td>1.313171</td>\n",
" <td>2.021121</td>\n",
" <td>0.048005</td>\n",
" <td>-4.580225</td>\n",
" <td>LOC283868</td>\n",
" <td>None</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>BEND6\\1568820_a_at</th>\n",
" <td>-0.943036</td>\n",
" <td>-2.019456</td>\n",
" <td>0.048183</td>\n",
" <td>-4.580256</td>\n",
" <td>BEND6</td>\n",
" <td>221336</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>C21orf94\\1553519_at</th>\n",
" <td>-1.175958</td>\n",
" <td>-2.016891</td>\n",
" <td>0.048458</td>\n",
" <td>-4.580303</td>\n",
" <td>C21orf94</td>\n",
" <td>None</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ACTL9\\243208_x_at</th>\n",
" <td>1.103029</td>\n",
" <td>2.010967</td>\n",
" <td>0.049099</td>\n",
" <td>-4.580413</td>\n",
" <td>ACTL9</td>\n",
" <td>284382</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>EFCAB6\\234732_s_at</th>\n",
" <td>1.412526</td>\n",
" <td>2.006627</td>\n",
" <td>0.049574</td>\n",
" <td>-4.580493</td>\n",
" <td>EFCAB6</td>\n",
" <td>64800</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>KDSR\\222359_x_at</th>\n",
" <td>1.343963</td>\n",
" <td>2.006528</td>\n",
" <td>0.049585</td>\n",
" <td>-4.580495</td>\n",
" <td>KDSR</td>\n",
" <td>2531</td>\n",
" <td>[<a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa00600+2531\">hsa00600</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa01100+2531\">hsa01100</a>]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>LOC100506920\\237659_at</th>\n",
" <td>0.776889</td>\n",
" <td>2.005503</td>\n",
" <td>0.049697</td>\n",
" <td>-4.580514</td>\n",
" <td>LOC100506920</td>\n",
" <td>None</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SHMT1\\231701_s_at</th>\n",
" <td>-1.117987</td>\n",
" <td>-2.004808</td>\n",
" <td>0.049774</td>\n",
" <td>-4.580527</td>\n",
" <td>SHMT1</td>\n",
" <td>6470</td>\n",
" <td>[<a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa00260+6470\">hsa00260</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa00460+6470\">hsa00460</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa00630+6470\">hsa00630</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa00670+6470\">hsa00670</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa01100+6470\">hsa01100</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa01130+6470\">hsa01130</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa01200+6470\">hsa01200</a>, <a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa01230+6470\">hsa01230</a>]</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>"
],
"text/plain": [
"<IPython.core.display.HTML object>"
]
},
"execution_count": 60,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from utils import Kegg\n",
"# find the pathways in KEGG that match one or more of the gene_ids:\n",
"kegg = Kegg(gene_ids = top_probes.gene_id)\n",
"\n",
"top_probes['pathways_ids'] = top_probes.gene_id.map(kegg.get_pathways_image_links_by_gene)\n",
"\n",
"from IPython.display import HTML\n",
"HTML(top_probes.to_html(escape=False))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Results + KEGG visualization\n",
"Here we select the pathways that match 2 or more genes. The pathway name is also a link to the KEGG visualization, which displays the pathway and all the genes of our dataset that were found in this pathway. The genes of our dataset are highlighted in red in the KEGG visualization. The figure below shows this.\n",
"\n",
"<img style=\"float: left;\" src=\"files/hsa04723.png\">"
]
},
{
"cell_type": "code",
"execution_count": 61,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>link to pathway</th>\n",
" <th>nr genes matched</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>42</th>\n",
" <td><a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05202+862+4094+2892+6757\">hsa05202</a></td>\n",
" <td>4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>65</th>\n",
" <td><a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04080+2892+5618+2898\">hsa04080</a></td>\n",
" <td>3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
" <td><a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04060+27190+5618+3558\">hsa04060</a></td>\n",
" <td>3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>56</th>\n",
" <td><a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa01100+5313+6470+2531\">hsa01100</a></td>\n",
" <td>3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>53</th>\n",
" <td><a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04151+5618+7249+3558\">hsa04151</a></td>\n",
" <td>3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>40</th>\n",
" <td><a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05200+862+7188\">hsa05200</a></td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>62</th>\n",
" <td><a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa00230+5145+5313\">hsa00230</a></td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>45</th>\n",
" <td><a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04910+5313+7249\">hsa04910</a></td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>41</th>\n",
" <td><a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05203+23352+7188\">hsa05203</a></td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td><a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04630+5618+3558\">hsa04630</a></td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td><a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04744+5145+131890\">hsa04744</a></td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>32</th>\n",
" <td><a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04144+131890+26052\">hsa04144</a></td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>29</th>\n",
" <td><a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa01230+5313+6470\">hsa01230</a></td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>28</th>\n",
" <td><a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa01130+5313+6470\">hsa01130</a></td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>22</th>\n",
" <td><a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa01200+5313+6470\">hsa01200</a></td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>19</th>\n",
" <td><a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04919+8202+7249\">hsa04919</a></td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td><a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa04724+2892+2898\">hsa04724</a></td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>39</th>\n",
" <td><a target=\"_blank\" href=\"http://www.kegg.jp/pathway/hsa05321+4094+3558\">hsa05321</a></td>\n",
" <td>2</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>"
],
"text/plain": [
"<IPython.core.display.HTML object>"
]
},
"execution_count": 61,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"pathways_df = DataFrame(kegg.get_all_pathways_rows(), columns=['link to pathway', 'nr genes matched'])\n",
"\n",
"pathways_df = pathways_df[pathways_df['nr genes matched'] > 1].sort(['nr genes matched'], ascending = False)\n",
"\n",
"HTML(pathways_df.to_html(escape=False))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Exercise \n",
"------------------------\n",
"Change p-value constraint to 0.05 in step [Filtering results on p-value](#Filtering-results-on-p-value)\n"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"# optional exercise: duplicate only the necessary code here, now with new p-value. \n",
"# Generate only the table with the list of pathways and 'nr of genes matched' "
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 2",
"language": "python",
"name": "python2"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.10"
}
},
"nbformat": 4,
"nbformat_minor": 0
}
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