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kellrott/RNA-Compare.ipynb

Created August 16, 2017 13:34
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RNA-Compare.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 16,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"%matplotlib inline"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"import ophion\n",
"import json\n",
"import matplotlib.pyplot as plt\n",
"import pandas"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"from scipy.stats import expon\n",
"\n",
"def exp_norm(matrix):\n",
" out = matrix.apply(lambda x: expon.ppf( (x.rank()-1) / len(x) ), 1)\n",
" return out.fillna(0.0)"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"from scipy.spatial import distance\n",
"import numpy as np"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"O = ophion.Ophion(\"http://bmeg.compbio.ohsu.edu\")"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"data = {}\n",
"for i in O.query().has(\"gid\", \"cohort:CCLE\").outgoing(\"hasSample\").incoming(\"expressionForSample\").execute():\n",
" if 'properties' in i and 'serializedExpressions' in i['properties']:\n",
" s = json.loads(i['properties']['serializedExpressions'])\n",
" data[i['gid']] = s\n",
"\n",
"exp = pandas.DataFrame(data).transpose()"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"[{u'gid': u'individualCohort:TCGA-ACC',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-ACC',\n",
" u'name': u'TCGA-ACC'}},\n",
" {u'gid': u'individualCohort:TCGA-KICH',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-KICH',\n",
" u'name': u'TCGA-KICH'}},\n",
" {u'gid': u'individualCohort:TCGA-UVM',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-UVM',\n",
" u'name': u'TCGA-UVM'}},\n",
" {u'gid': u'individualCohort:TCGA-PRAD',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-PRAD',\n",
" u'name': u'TCGA-PRAD'}},\n",
" {u'gid': u'individualCohort:TCGA-LGG',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-LGG',\n",
" u'name': u'TCGA-LGG'}},\n",
" {u'gid': u'individualCohort:TCGA-SKCM',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-SKCM',\n",
" u'name': u'TCGA-SKCM'}},\n",
" {u'gid': u'individualCohort:TCGA-HNSC',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-HNSC',\n",
" u'name': u'TCGA-HNSC'}},\n",
" {u'gid': u'individualCohort:TCGA-BLCA',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-BLCA',\n",
" u'name': u'TCGA-BLCA'}},\n",
" {u'gid': u'individualCohort:TCGA-LIHC',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-LIHC',\n",
" u'name': u'TCGA-LIHC'}},\n",
" {u'gid': u'individualCohort:TCGA-MESO',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-MESO',\n",
" u'name': u'TCGA-MESO'}},\n",
" {u'gid': u'individualCohort:TCGA-LAML',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-LAML',\n",
" u'name': u'TCGA-LAML'}},\n",
" {u'gid': u'individualCohort:TCGA-LUAD',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-LUAD',\n",
" u'name': u'TCGA-LUAD'}},\n",
" {u'gid': u'individualCohort:TCGA-THYM',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-THYM',\n",
" u'name': u'TCGA-THYM'}},\n",
" {u'gid': u'individualCohort:TCGA-LUSC',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-LUSC',\n",
" u'name': u'TCGA-LUSC'}},\n",
" {u'gid': u'individualCohort:TCGA-PCPG',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-PCPG',\n",
" u'name': u'TCGA-PCPG'}},\n",
" {u'gid': u'individualCohort:TCGA-KIRC',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-KIRC',\n",
" u'name': u'TCGA-KIRC'}},\n",
" {u'gid': u'individualCohort:TCGA-CHOL',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-CHOL',\n",
" u'name': u'TCGA-CHOL'}},\n",
" {u'gid': u'individualCohort:TCGA-CESC',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-CESC',\n",
" u'name': u'TCGA-CESC'}},\n",
" {u'gid': u'individualCohort:TCGA-BRCA',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-BRCA',\n",
" u'name': u'TCGA-BRCA'}},\n",
" {u'gid': u'individualCohort:TCGA-TGCT',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-TGCT',\n",
" u'name': u'TCGA-TGCT'}},\n",
" {u'gid': u'individualCohort:TCGA-PAAD',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-PAAD',\n",
" u'name': u'TCGA-PAAD'}},\n",
" {u'gid': u'individualCohort:TCGA-GBM',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-GBM',\n",
" u'name': u'TCGA-GBM'}},\n",
" {u'gid': u'individualCohort:TCGA-DLBC',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-DLBC',\n",
" u'name': u'TCGA-DLBC'}},\n",
" {u'gid': u'individualCohort:TCGA-OV',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-OV',\n",
" u'name': u'TCGA-OV'}},\n",
" {u'gid': u'individualCohort:TCGA-COAD',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-COAD',\n",
" u'name': u'TCGA-COAD'}},\n",
" {u'gid': u'individualCohort:TCGA-UCS',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-UCS',\n",
" u'name': u'TCGA-UCS'}},\n",
" {u'gid': u'individualCohort:TCGA-SARC',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-SARC',\n",
" u'name': u'TCGA-SARC'}},\n",
" {u'gid': u'individualCohort:TCGA-KIRP',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-KIRP',\n",
" u'name': u'TCGA-KIRP'}},\n",
" {u'gid': u'individualCohort:TCGA-ESCA',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-ESCA',\n",
" u'name': u'TCGA-ESCA'}},\n",
" {u'gid': u'individualCohort:TCGA-THCA',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-THCA',\n",
" u'name': u'TCGA-THCA'}},\n",
" {u'gid': u'individualCohort:TCGA-STAD',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-STAD',\n",
" u'name': u'TCGA-STAD'}},\n",
" {u'gid': u'individualCohort:TCGA-READ',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-READ',\n",
" u'name': u'TCGA-READ'}},\n",
" {u'gid': u'individualCohort:TCGA-UCEC',\n",
" u'label': u'IndividualCohort',\n",
" u'properties': {u'#label': u'IndividualCohort',\n",
" u'id': u'individualCohort:TCGA-UCEC',\n",
" u'name': u'TCGA-UCEC'}}]"
]
},
"execution_count": 22,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"O.query().has(\"gid\", \"type:IndividualCohort\").outgoing(\"hasInstance\").execute()"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"data = {}\n",
"for i in O.query().has(\"gid\", \"individualCohort:TCGA-PAAD\").outgoing(\"hasMember\").incoming(\"biosampleOfIndividual\").incoming(\"expressionForSample\").execute():\n",
" if 'properties' in i and 'serializedExpressions' in i['properties']:\n",
" s = json.loads(i['properties']['serializedExpressions'])\n",
" data[i['gid']] = s\n",
"samples = pandas.DataFrame(data).transpose()"
]
},
{
"cell_type": "code",
"execution_count": 24,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"isect = exp.columns.intersection(samples.columns)"
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/usr/local/lib/python2.7/site-packages/scipy/stats/_distn_infrastructure.py:1897: RuntimeWarning: invalid value encountered in greater\n",
" cond1 = (0 < q) & (q < 1)\n",
"/usr/local/lib/python2.7/site-packages/scipy/stats/_distn_infrastructure.py:1897: RuntimeWarning: invalid value encountered in less\n",
" cond1 = (0 < q) & (q < 1)\n"
]
}
],
"source": [
"exp_isect = exp_norm( exp.reindex(columns=isect) )\n",
"samples_isect = exp_norm( samples.reindex(columns=isect) )"
]
},
{
"cell_type": "code",
"execution_count": 26,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"dist_matrix = exp_isect.apply( lambda x: samples_isect.apply(lambda y: distance.euclidean(x,y), 1 ), 1 )"
]
},
{
"cell_type": "code",
"execution_count": 27,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"matches = {}\n",
"for i in set( dist_matrix.index.map( lambda x: x.split(\"_\", 1)[1] ) ):\n",
" matches[i] = dist_matrix.index.map( lambda x: x.split(\"_\", 1)[1] == i )"
]
},
{
"cell_type": "code",
"execution_count": 34,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"matches = dict(filter(lambda x: sum(x[1]) >= 20, matches.items()))"
]
},
{
"cell_type": "code",
"execution_count": 35,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"from scipy.stats import ttest_ind"
]
},
{
"cell_type": "code",
"execution_count": 36,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"(array([ 6., 13., 21., 20., 21., 17., 12., 10., 13., 12., 5.,\n",
" 2., 3., 0., 0., 0., 3., 3., 0., 3.]),\n",
" array([-8.5886319 , -8.15365079, -7.71866968, -7.28368856, -6.84870745,\n",
" -6.41372634, -5.97874522, -5.54376411, -5.108783 , -4.67380188,\n",
" -4.23882077, -3.80383966, -3.36885854, -2.93387743, -2.49889632,\n",
" -2.0639152 , -1.62893409, -1.19395298, -0.75897186, -0.32399075,\n",
" 0.11099036]),\n",
" <a list of 20 Patch objects>)"
]
},
"execution_count": 36,
"metadata": {},
"output_type": "execute_result"
},
{
"data": {
"image/png": 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+K8mbp/1YwKTmkvhDG3owjc/h/0JV/WBVfUdVPTXJOzL6WN7See4KAEzJNPbwvz3JW5M8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\nQAcEHwA68P8BO4QzvVxFd0YAAAAASUVORK5CYII=\n",
"text/plain": [
"<matplotlib.figure.Figure at 0x1166e7110>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"e = ttest_ind( dist_matrix.loc[matches[\"PANCREAS\"]], dist_matrix[~matches[\"PANCREAS\"]], axis=0 )\n",
"plt.hist(e.statistic, bins=20)"
]
},
{
"cell_type": "code",
"execution_count": 47,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"[u'UPPER_AERODIGESTIVE_TRACT',\n",
" u'LARGE_INTESTINE',\n",
" u'STOMACH',\n",
" u'SOFT_TISSUE',\n",
" u'CENTRAL_NERVOUS_SYSTEM',\n",
" u'HAEMATOPOIETIC_AND_LYMPHOID_TISSUE',\n",
" u'ENDOMETRIUM',\n",
" u'URINARY_TRACT',\n",
" u'BONE',\n",
" u'LUNG',\n",
" u'LIVER',\n",
" u'SKIN',\n",
" u'OESOPHAGUS',\n",
" u'OVARY',\n",
" u'PANCREAS',\n",
" u'KIDNEY',\n",
" u'BREAST']"
]
},
"execution_count": 47,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"matches.keys()"
]
},
{
"cell_type": "code",
"execution_count": 48,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"<matplotlib.legend.Legend at 0x116cd8250>"
]
},
"execution_count": 48,
"metadata": {},
"output_type": "execute_result"
},
{
"data": {
"image/png": 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3HllZWZgZa9asYdu2bdUqJFaZM2cOQ4cOjeu5NCWaQyAiIs2Kcy707927d3Po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\n",
"text/plain": [
"<matplotlib.figure.Figure at 0x125ec7b50>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"plt.figure()\n",
"for k in ['PANCREAS','KIDNEY','BREAST','LUNG','STOMACH','SKIN','BONE']:\n",
" #if k != \"PANCREAS\":\n",
" e = ttest_ind( dist_matrix.loc[matches[k]], dist_matrix[~matches[k]], axis=0 )\n",
" p = plt.hist(e.statistic, bins=50, range=[-20,20], label=k)\n",
" #lps.append(p[1])\n",
"plt.legend(fontsize = 'x-small')"
]
},
{
"cell_type": "code",
"execution_count": 32,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"(array([ 6., 13., 21., 20., 21., 17., 12., 10., 13., 12., 5.,\n",
" 2., 3., 0., 0., 0., 3., 3., 0., 3.]),\n",
" array([-8.5886319 , -8.15365079, -7.71866968, -7.28368856, -6.84870745,\n",
" -6.41372634, -5.97874522, -5.54376411, -5.108783 , -4.67380188,\n",
" -4.23882077, -3.80383966, -3.36885854, -2.93387743, -2.49889632,\n",
" -2.0639152 , -1.62893409, -1.19395298, -0.75897186, -0.32399075,\n",
" 0.11099036]),\n",
" <a list of 20 Patch objects>)"
]
},
"execution_count": 32,
"metadata": {},
"output_type": "execute_result"
},
{
"data": {
"image/png": 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"text/plain": [
"<matplotlib.figure.Figure at 0x13fea1850>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"k=\"PANCREAS\"\n",
"e = ttest_ind( dist_matrix.loc[matches[k]], dist_matrix[~matches[k]], axis=0 )\n",
"plt.hist(e.statistic, bins=20)"
]
},
{
"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>geneExpression:biosample:TCGA-PAAD:TCGA-2J-AAB4-01A</th>\n",
" <th>geneExpression:biosample:TCGA-PAAD:TCGA-2J-AAB6-01A</th>\n",
" <th>geneExpression:biosample:TCGA-PAAD:TCGA-2J-AAB8-01A</th>\n",
" <th>geneExpression:biosample:TCGA-PAAD:TCGA-2J-AAB9-01A</th>\n",
" <th>geneExpression:biosample:TCGA-PAAD:TCGA-2J-AABA-01A</th>\n",
" <th>geneExpression:biosample:TCGA-PAAD:TCGA-2J-AABE-01A</th>\n",
" <th>geneExpression:biosample:TCGA-PAAD:TCGA-2J-AABH-01A</th>\n",
" <th>geneExpression:biosample:TCGA-PAAD:TCGA-2J-AABK-01A</th>\n",
" <th>geneExpression:biosample:TCGA-PAAD:TCGA-2J-AABO-01A</th>\n",
" <th>geneExpression:biosample:TCGA-PAAD:TCGA-2J-AABR-01A</th>\n",
" <th>...</th>\n",
" <th>geneExpression:biosample:TCGA-PAAD:TCGA-XD-AAUG-01A</th>\n",
" <th>geneExpression:biosample:TCGA-PAAD:TCGA-XD-AAUH-01A</th>\n",
" <th>geneExpression:biosample:TCGA-PAAD:TCGA-XD-AAUL-01A</th>\n",
" <th>geneExpression:biosample:TCGA-PAAD:TCGA-XN-A8T3-01A</th>\n",
" <th>geneExpression:biosample:TCGA-PAAD:TCGA-XN-A8T5-01A</th>\n",
" <th>geneExpression:biosample:TCGA-PAAD:TCGA-YB-A89D-01A</th>\n",
" <th>geneExpression:biosample:TCGA-PAAD:TCGA-YB-A89D-11A</th>\n",
" <th>geneExpression:biosample:TCGA-PAAD:TCGA-YH-A8SY-01A</th>\n",
" <th>geneExpression:biosample:TCGA-PAAD:TCGA-YY-A8LH-01A</th>\n",
" <th>geneExpression:biosample:TCGA-PAAD:TCGA-Z5-AAPL-01A</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>geneExpression:CFPAC1_PANCREAS</th>\n",
" <td>99.885772</td>\n",
" <td>98.753630</td>\n",
" <td>99.454590</td>\n",
" <td>102.160668</td>\n",
" <td>101.118237</td>\n",
" <td>101.690497</td>\n",
" <td>100.768561</td>\n",
" <td>97.431114</td>\n",
" <td>99.187374</td>\n",
" <td>102.175875</td>\n",
" <td>...</td>\n",
" <td>106.201782</td>\n",
" <td>104.620828</td>\n",
" <td>100.277148</td>\n",
" <td>99.845229</td>\n",
" <td>102.752871</td>\n",
" <td>101.747233</td>\n",
" <td>103.398924</td>\n",
" <td>99.636751</td>\n",
" <td>97.466720</td>\n",
" <td>102.626598</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:ASPC1_PANCREAS</th>\n",
" <td>99.937049</td>\n",
" <td>100.449062</td>\n",
" <td>98.649278</td>\n",
" <td>101.954107</td>\n",
" <td>99.617335</td>\n",
" <td>100.880879</td>\n",
" <td>99.093886</td>\n",
" <td>96.602577</td>\n",
" <td>99.596247</td>\n",
" <td>102.521829</td>\n",
" <td>...</td>\n",
" <td>105.944113</td>\n",
" <td>104.218458</td>\n",
" <td>100.315369</td>\n",
" <td>101.161861</td>\n",
" <td>102.475608</td>\n",
" <td>100.980074</td>\n",
" <td>103.287674</td>\n",
" <td>99.946336</td>\n",
" <td>94.861615</td>\n",
" <td>102.941663</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:CL40_LARGE_INTESTINE</th>\n",
" <td>100.216265</td>\n",
" <td>100.746794</td>\n",
" <td>99.290526</td>\n",
" <td>102.430056</td>\n",
" <td>100.346610</td>\n",
" <td>101.671951</td>\n",
" <td>99.758752</td>\n",
" <td>96.284211</td>\n",
" <td>100.004418</td>\n",
" <td>102.928758</td>\n",
" <td>...</td>\n",
" <td>106.976697</td>\n",
" <td>105.334621</td>\n",
" <td>101.049711</td>\n",
" <td>101.603513</td>\n",
" <td>103.967580</td>\n",
" <td>101.909238</td>\n",
" <td>104.511618</td>\n",
" <td>100.470935</td>\n",
" <td>95.577991</td>\n",
" <td>103.665731</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:UMUC1_URINARY_TRACT</th>\n",
" <td>100.887093</td>\n",
" <td>98.357579</td>\n",
" <td>99.424049</td>\n",
" <td>101.158184</td>\n",
" <td>100.407280</td>\n",
" <td>101.595324</td>\n",
" <td>100.305637</td>\n",
" <td>98.125407</td>\n",
" <td>99.050679</td>\n",
" <td>102.263843</td>\n",
" <td>...</td>\n",
" <td>105.498853</td>\n",
" <td>103.935502</td>\n",
" <td>101.086867</td>\n",
" <td>99.297808</td>\n",
" <td>102.384182</td>\n",
" <td>101.683381</td>\n",
" <td>102.916387</td>\n",
" <td>98.455259</td>\n",
" <td>97.835312</td>\n",
" <td>102.980802</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:SNU213_PANCREAS</th>\n",
" <td>100.901650</td>\n",
" <td>99.134560</td>\n",
" <td>100.411750</td>\n",
" <td>102.666474</td>\n",
" <td>101.674567</td>\n",
" <td>103.100878</td>\n",
" <td>101.421812</td>\n",
" <td>98.861567</td>\n",
" <td>100.545986</td>\n",
" <td>103.023237</td>\n",
" <td>...</td>\n",
" <td>107.009162</td>\n",
" <td>105.452082</td>\n",
" <td>101.343536</td>\n",
" <td>100.790102</td>\n",
" <td>103.756973</td>\n",
" <td>102.824738</td>\n",
" <td>104.392695</td>\n",
" <td>100.728144</td>\n",
" <td>99.191725</td>\n",
" <td>103.392270</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:SNU601_STOMACH</th>\n",
" <td>100.922547</td>\n",
" <td>100.297804</td>\n",
" <td>99.341955</td>\n",
" <td>102.912283</td>\n",
" <td>101.656636</td>\n",
" <td>102.195876</td>\n",
" <td>100.305757</td>\n",
" <td>96.834596</td>\n",
" <td>100.562018</td>\n",
" <td>103.797638</td>\n",
" <td>...</td>\n",
" <td>107.182915</td>\n",
" <td>105.388219</td>\n",
" <td>102.118701</td>\n",
" <td>101.436131</td>\n",
" <td>104.086315</td>\n",
" <td>102.854730</td>\n",
" <td>105.054476</td>\n",
" <td>100.219105</td>\n",
" <td>96.516871</td>\n",
" <td>102.313758</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:PANC0504_PANCREAS</th>\n",
" <td>100.945152</td>\n",
" <td>99.039704</td>\n",
" <td>99.981622</td>\n",
" <td>102.578063</td>\n",
" <td>101.079756</td>\n",
" <td>102.464431</td>\n",
" <td>100.705010</td>\n",
" <td>98.147242</td>\n",
" <td>99.825180</td>\n",
" <td>103.194430</td>\n",
" <td>...</td>\n",
" <td>106.972025</td>\n",
" <td>105.357826</td>\n",
" <td>101.223228</td>\n",
" <td>101.101008</td>\n",
" <td>103.574575</td>\n",
" <td>102.273374</td>\n",
" <td>104.400100</td>\n",
" <td>99.928609</td>\n",
" <td>97.587090</td>\n",
" <td>103.207733</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:HPAFII_PANCREAS</th>\n",
" <td>100.957443</td>\n",
" <td>100.208342</td>\n",
" <td>99.706896</td>\n",
" <td>103.062689</td>\n",
" <td>101.081812</td>\n",
" <td>102.321181</td>\n",
" <td>100.700340</td>\n",
" <td>97.557664</td>\n",
" <td>100.414513</td>\n",
" <td>103.463459</td>\n",
" <td>...</td>\n",
" <td>107.651761</td>\n",
" <td>105.717395</td>\n",
" <td>101.263772</td>\n",
" <td>101.793805</td>\n",
" <td>103.932233</td>\n",
" <td>102.369448</td>\n",
" <td>104.574011</td>\n",
" <td>100.738304</td>\n",
" <td>96.000872</td>\n",
" <td>103.567283</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:HS604T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE</th>\n",
" <td>101.316617</td>\n",
" <td>99.173690</td>\n",
" <td>98.451391</td>\n",
" <td>100.498457</td>\n",
" <td>100.101804</td>\n",
" <td>101.632964</td>\n",
" <td>101.873523</td>\n",
" <td>100.169266</td>\n",
" <td>98.689213</td>\n",
" <td>101.109006</td>\n",
" <td>...</td>\n",
" <td>99.212617</td>\n",
" <td>100.382371</td>\n",
" <td>100.223326</td>\n",
" <td>98.198936</td>\n",
" <td>98.296993</td>\n",
" <td>99.839302</td>\n",
" <td>99.210102</td>\n",
" <td>98.010451</td>\n",
" <td>102.624929</td>\n",
" <td>102.001032</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:SNU1197_LARGE_INTESTINE</th>\n",
" <td>101.351076</td>\n",
" <td>98.404850</td>\n",
" <td>100.005367</td>\n",
" <td>102.916777</td>\n",
" <td>101.940190</td>\n",
" <td>103.222078</td>\n",
" <td>101.792490</td>\n",
" <td>99.099291</td>\n",
" <td>100.456267</td>\n",
" <td>103.772708</td>\n",
" <td>...</td>\n",
" <td>107.213695</td>\n",
" <td>105.372430</td>\n",
" <td>101.771856</td>\n",
" <td>101.252624</td>\n",
" <td>103.177698</td>\n",
" <td>103.056230</td>\n",
" <td>104.481311</td>\n",
" <td>100.339988</td>\n",
" <td>98.527437</td>\n",
" <td>102.852867</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:PANC0213_PANCREAS</th>\n",
" <td>101.491574</td>\n",
" <td>99.312056</td>\n",
" <td>100.629569</td>\n",
" <td>103.089831</td>\n",
" <td>101.960931</td>\n",
" <td>103.124035</td>\n",
" <td>101.414865</td>\n",
" <td>100.507933</td>\n",
" <td>101.254047</td>\n",
" <td>103.111489</td>\n",
" <td>...</td>\n",
" <td>106.386553</td>\n",
" <td>104.999776</td>\n",
" <td>102.145282</td>\n",
" <td>100.995526</td>\n",
" <td>103.600892</td>\n",
" <td>103.003282</td>\n",
" <td>104.044898</td>\n",
" <td>100.530981</td>\n",
" <td>100.259549</td>\n",
" <td>104.005952</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:BXPC3_PANCREAS</th>\n",
" <td>101.561461</td>\n",
" <td>97.676037</td>\n",
" <td>100.298063</td>\n",
" <td>102.387253</td>\n",
" <td>101.974429</td>\n",
" <td>102.952913</td>\n",
" <td>101.684136</td>\n",
" <td>98.581773</td>\n",
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" <td>102.878417</td>\n",
" <td>...</td>\n",
" <td>106.906513</td>\n",
" <td>105.335914</td>\n",
" <td>101.548963</td>\n",
" <td>100.755177</td>\n",
" <td>103.453188</td>\n",
" <td>102.289526</td>\n",
" <td>103.881916</td>\n",
" <td>98.960290</td>\n",
" <td>98.333685</td>\n",
" <td>102.885398</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:SU8686_PANCREAS</th>\n",
" <td>101.599559</td>\n",
" <td>100.772107</td>\n",
" <td>101.043951</td>\n",
" <td>103.736189</td>\n",
" <td>102.399640</td>\n",
" <td>103.717102</td>\n",
" <td>102.480838</td>\n",
" <td>100.135879</td>\n",
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" <td>103.489399</td>\n",
" <td>...</td>\n",
" <td>106.634710</td>\n",
" <td>105.340562</td>\n",
" <td>102.345752</td>\n",
" <td>101.866770</td>\n",
" <td>104.076107</td>\n",
" <td>103.406982</td>\n",
" <td>104.948506</td>\n",
" <td>101.881528</td>\n",
" <td>100.346195</td>\n",
" <td>104.132469</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:SCC15_UPPER_AERODIGESTIVE_TRACT</th>\n",
" <td>101.686609</td>\n",
" <td>98.078604</td>\n",
" <td>100.081389</td>\n",
" <td>102.348856</td>\n",
" <td>101.950116</td>\n",
" <td>103.334518</td>\n",
" <td>102.378757</td>\n",
" <td>99.895294</td>\n",
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" <td>102.435418</td>\n",
" <td>...</td>\n",
" <td>105.310009</td>\n",
" <td>104.411110</td>\n",
" <td>101.640323</td>\n",
" <td>99.955779</td>\n",
" <td>102.952886</td>\n",
" <td>102.323070</td>\n",
" <td>103.135622</td>\n",
" <td>99.157031</td>\n",
" <td>101.151156</td>\n",
" <td>102.905314</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:CAPAN1_PANCREAS</th>\n",
" <td>101.746378</td>\n",
" <td>101.663435</td>\n",
" <td>100.583939</td>\n",
" <td>103.735838</td>\n",
" <td>101.967829</td>\n",
" <td>103.380533</td>\n",
" <td>101.443337</td>\n",
" <td>98.472927</td>\n",
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" <td>104.334779</td>\n",
" <td>...</td>\n",
" <td>108.100577</td>\n",
" <td>106.122220</td>\n",
" <td>102.962924</td>\n",
" <td>102.292692</td>\n",
" <td>105.304897</td>\n",
" <td>104.086076</td>\n",
" <td>106.035732</td>\n",
" <td>101.972641</td>\n",
" <td>97.972534</td>\n",
" <td>103.968304</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:CAL33_UPPER_AERODIGESTIVE_TRACT</th>\n",
" <td>101.787410</td>\n",
" <td>100.041100</td>\n",
" <td>100.820506</td>\n",
" <td>103.184201</td>\n",
" <td>102.359297</td>\n",
" <td>103.438772</td>\n",
" <td>102.221713</td>\n",
" <td>99.154449</td>\n",
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" <td>...</td>\n",
" <td>107.297067</td>\n",
" <td>106.147551</td>\n",
" <td>102.453982</td>\n",
" <td>101.116917</td>\n",
" <td>104.565366</td>\n",
" <td>103.139630</td>\n",
" <td>104.773348</td>\n",
" <td>100.141273</td>\n",
" <td>100.035659</td>\n",
" <td>103.469534</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:SNU869_BILIARY_TRACT</th>\n",
" <td>101.842617</td>\n",
" <td>101.940657</td>\n",
" <td>101.337219</td>\n",
" <td>104.096998</td>\n",
" <td>102.658296</td>\n",
" <td>103.966617</td>\n",
" <td>103.172709</td>\n",
" <td>99.339863</td>\n",
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" <td>...</td>\n",
" <td>108.051461</td>\n",
" <td>106.347789</td>\n",
" <td>102.955288</td>\n",
" <td>101.855358</td>\n",
" <td>104.535474</td>\n",
" <td>104.351530</td>\n",
" <td>106.090676</td>\n",
" <td>102.847765</td>\n",
" <td>99.831622</td>\n",
" <td>104.341069</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:SNU1076_UPPER_AERODIGESTIVE_TRACT</th>\n",
" <td>101.966400</td>\n",
" <td>100.041194</td>\n",
" <td>101.005647</td>\n",
" <td>103.222765</td>\n",
" <td>102.157297</td>\n",
" <td>103.768987</td>\n",
" <td>102.875923</td>\n",
" <td>100.027256</td>\n",
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" <td>...</td>\n",
" <td>107.094412</td>\n",
" <td>105.710964</td>\n",
" <td>102.654352</td>\n",
" <td>100.437642</td>\n",
" <td>104.269119</td>\n",
" <td>103.473633</td>\n",
" <td>104.744775</td>\n",
" <td>100.914845</td>\n",
" <td>100.944104</td>\n",
" <td>103.827220</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:CAPAN2_PANCREAS</th>\n",
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" <td>99.854306</td>\n",
" <td>100.754865</td>\n",
" <td>103.533590</td>\n",
" <td>102.351849</td>\n",
" <td>103.599890</td>\n",
" <td>101.798946</td>\n",
" <td>99.398595</td>\n",
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" <td>...</td>\n",
" <td>108.219976</td>\n",
" <td>106.316381</td>\n",
" <td>102.772503</td>\n",
" <td>101.381669</td>\n",
" <td>104.487675</td>\n",
" <td>103.919834</td>\n",
" <td>105.680639</td>\n",
" <td>101.252734</td>\n",
" <td>98.439361</td>\n",
" <td>103.845722</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:TCCPAN2_PANCREAS</th>\n",
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" <td>99.720675</td>\n",
" <td>102.594623</td>\n",
" <td>101.181190</td>\n",
" <td>102.861655</td>\n",
" <td>100.931668</td>\n",
" <td>97.740461</td>\n",
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" <td>...</td>\n",
" <td>106.123063</td>\n",
" <td>104.627862</td>\n",
" <td>102.010008</td>\n",
" <td>100.819378</td>\n",
" <td>103.049602</td>\n",
" <td>102.506541</td>\n",
" <td>103.972801</td>\n",
" <td>100.466892</td>\n",
" <td>97.160055</td>\n",
" <td>102.811149</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:BICR56_UPPER_AERODIGESTIVE_TRACT</th>\n",
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" <td>101.045886</td>\n",
" <td>103.154127</td>\n",
" <td>102.432951</td>\n",
" <td>103.293433</td>\n",
" <td>102.527661</td>\n",
" <td>99.876811</td>\n",
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" <td>...</td>\n",
" <td>106.662637</td>\n",
" <td>105.594750</td>\n",
" <td>102.004795</td>\n",
" <td>102.064450</td>\n",
" <td>104.053892</td>\n",
" <td>103.031063</td>\n",
" <td>104.249178</td>\n",
" <td>100.075582</td>\n",
" <td>100.696093</td>\n",
" <td>104.257396</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:SNU899_UPPER_AERODIGESTIVE_TRACT</th>\n",
" <td>102.093306</td>\n",
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" <td>100.985071</td>\n",
" <td>103.259417</td>\n",
" <td>102.612777</td>\n",
" <td>103.822652</td>\n",
" <td>102.321781</td>\n",
" <td>100.014745</td>\n",
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" <td>107.388354</td>\n",
" <td>105.855072</td>\n",
" <td>102.827657</td>\n",
" <td>101.413834</td>\n",
" <td>104.395182</td>\n",
" <td>103.731053</td>\n",
" <td>105.149123</td>\n",
" <td>100.490433</td>\n",
" <td>100.243102</td>\n",
" <td>103.499550</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:BICR22_UPPER_AERODIGESTIVE_TRACT</th>\n",
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" <td>103.748251</td>\n",
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" <td>107.895162</td>\n",
" <td>106.543458</td>\n",
" <td>102.821300</td>\n",
" <td>102.201051</td>\n",
" <td>104.866751</td>\n",
" <td>103.634555</td>\n",
" <td>105.136079</td>\n",
" <td>100.295761</td>\n",
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" <td>104.241028</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:CAL851_BREAST</th>\n",
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" <td>102.714014</td>\n",
" <td>102.648335</td>\n",
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" <td>106.936265</td>\n",
" <td>105.389801</td>\n",
" <td>102.391289</td>\n",
" <td>100.684342</td>\n",
" <td>103.716586</td>\n",
" <td>103.555006</td>\n",
" <td>104.358950</td>\n",
" <td>100.300546</td>\n",
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" <td>103.913419</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:SNU81_LARGE_INTESTINE</th>\n",
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" <td>100.449325</td>\n",
" <td>104.122268</td>\n",
" <td>102.293443</td>\n",
" <td>103.530071</td>\n",
" <td>102.009622</td>\n",
" <td>97.908333</td>\n",
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" <td>...</td>\n",
" <td>107.853447</td>\n",
" <td>106.022098</td>\n",
" <td>103.791330</td>\n",
" <td>102.772249</td>\n",
" <td>105.060061</td>\n",
" <td>104.132653</td>\n",
" <td>106.438994</td>\n",
" <td>102.475870</td>\n",
" <td>97.698416</td>\n",
" <td>103.686087</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:CAL27_UPPER_AERODIGESTIVE_TRACT</th>\n",
" <td>102.532127</td>\n",
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" <td>101.090701</td>\n",
" <td>103.670779</td>\n",
" <td>103.500903</td>\n",
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" <td>107.829679</td>\n",
" <td>106.392223</td>\n",
" <td>103.522616</td>\n",
" <td>101.560325</td>\n",
" <td>104.660778</td>\n",
" <td>103.962121</td>\n",
" <td>105.329807</td>\n",
" <td>100.322044</td>\n",
" <td>100.668554</td>\n",
" <td>103.121752</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneExpression:NCIH2444_LUNG</th>\n",
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"<p>1036 rows × 164 columns</p>\n",
"</div>"
],
"text/plain": [
" geneExpression:biosample:TCGA-PAAD:TCGA-2J-AAB4-01A \\\n",
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"... ... \n",
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"... ... \n",
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"... ... \n",
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"... ... \n",
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"... ... \n",
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"... ... \n",
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"... ... \n",
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"... ... \n",
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"\n",
" geneExpression:biosample:TCGA-PAAD:TCGA-2J-AABO-01A \\\n",
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"... ... \n",
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"\n",
" geneExpression:biosample:TCGA-PAAD:TCGA-2J-AABR-01A \\\n",
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"... ... \n",
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"geneExpression:NCIH292_LUNG 156.215238 \n",
"\n",
" ... \\\n",
"geneExpression:CFPAC1_PANCREAS ... \n",
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"geneExpression:CAPAN1_PANCREAS ... \n",
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"geneExpression:SNU869_BILIARY_TRACT ... \n",
"geneExpression:SNU1076_UPPER_AERODIGESTIVE_TRACT ... \n",
"geneExpression:CAPAN2_PANCREAS ... \n",
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"... ... \n",
"geneExpression:NCIH524_LUNG ... \n",
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"geneExpression:CORL24_LUNG ... \n",
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"\n",
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"... ... \n",
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"\n",
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"... ... \n",
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"geneExpression:NCIH1092_LUNG 117.523092 \n",
"geneExpression:NCIH292_LUNG 155.893638 \n",
"\n",
" geneExpression:biosample:TCGA-PAAD:TCGA-XD-AAUL-01A \\\n",
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"... ... \n",
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"... ... \n",
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"... ... \n",
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"... ... \n",
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"... ... \n",
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"... ... \n",
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"geneExpression:NCIH1436_LUNG 115.977416 \n",
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"geneExpression:PF382_HAEMATOPOIETIC_AND_LYMPHOI... 115.986378 \n",
"geneExpression:CA46_HAEMATOPOIETIC_AND_LYMPHOID... 115.609963 \n",
"geneExpression:SHSY5Y_AUTONOMIC_GANGLIA 115.222124 \n",
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"geneExpression:NCIH2227_LUNG 115.459713 \n",
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"geneExpression:NCIH1105_LUNG 118.026683 \n",
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"geneExpression:NCIH292_LUNG 155.738700 \n",
"\n",
" geneExpression:biosample:TCGA-PAAD:TCGA-YY-A8LH-01A \\\n",
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"geneExpression:UMUC1_URINARY_TRACT 97.835312 \n",
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"geneExpression:PANC0403_PANCREAS 98.841106 \n",
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"geneExpression:KCIMOH1_PANCREAS 99.655921 \n",
"... ... \n",
"geneExpression:NCIH524_LUNG 114.261216 \n",
"geneExpression:NCIH82_LUNG 113.783209 \n",
"geneExpression:MOLT4_HAEMATOPOIETIC_AND_LYMPHOI... 113.764354 \n",
"geneExpression:OCILY10_HAEMATOPOIETIC_AND_LYMPH... 113.222779 \n",
"geneExpression:SKNBE2_AUTONOMIC_GANGLIA 114.801037 \n",
"geneExpression:NCIH69_LUNG 114.574329 \n",
"geneExpression:NCIH1436_LUNG 115.017285 \n",
"geneExpression:KELLY_AUTONOMIC_GANGLIA 114.772018 \n",
"geneExpression:PF382_HAEMATOPOIETIC_AND_LYMPHOI... 115.042228 \n",
"geneExpression:CA46_HAEMATOPOIETIC_AND_LYMPHOID... 113.626487 \n",
"geneExpression:SHSY5Y_AUTONOMIC_GANGLIA 115.243040 \n",
"geneExpression:CPCN_LUNG 114.555675 \n",
"geneExpression:NCIH2227_LUNG 115.324365 \n",
"geneExpression:BL70_HAEMATOPOIETIC_AND_LYMPHOID... 113.834848 \n",
"geneExpression:D341MED_CENTRAL_NERVOUS_SYSTEM 114.548255 \n",
"geneExpression:NCIH1930_LUNG 115.056973 \n",
"geneExpression:NCIH2081_LUNG 115.302269 \n",
"geneExpression:NCIH1963_LUNG 115.527820 \n",
"geneExpression:SKNDZ_AUTONOMIC_GANGLIA 115.274973 \n",
"geneExpression:KPNRTBM1_AUTONOMIC_GANGLIA 116.108242 \n",
"geneExpression:CORL24_LUNG 116.748190 \n",
"geneExpression:KPNYN_AUTONOMIC_GANGLIA 116.346056 \n",
"geneExpression:NCIH1694_LUNG 115.903752 \n",
"geneExpression:HCC33_LUNG 116.364439 \n",
"geneExpression:IMR32_AUTONOMIC_GANGLIA 116.251722 \n",
"geneExpression:CHP126_AUTONOMIC_GANGLIA 116.147985 \n",
"geneExpression:NCIH1184_LUNG 116.553201 \n",
"geneExpression:NCIH1105_LUNG 117.430015 \n",
"geneExpression:NCIH1092_LUNG 117.968138 \n",
"geneExpression:NCIH292_LUNG 155.971042 \n",
"\n",
" geneExpression:biosample:TCGA-PAAD:TCGA-Z5-AAPL-01A \n",
"geneExpression:CFPAC1_PANCREAS 102.626598 \n",
"geneExpression:ASPC1_PANCREAS 102.941663 \n",
"geneExpression:CL40_LARGE_INTESTINE 103.665731 \n",
"geneExpression:UMUC1_URINARY_TRACT 102.980802 \n",
"geneExpression:SNU213_PANCREAS 103.392270 \n",
"geneExpression:SNU601_STOMACH 102.313758 \n",
"geneExpression:PANC0504_PANCREAS 103.207733 \n",
"geneExpression:HPAFII_PANCREAS 103.567283 \n",
"geneExpression:HS604T_HAEMATOPOIETIC_AND_LYMPHO... 102.001032 \n",
"geneExpression:SNU1197_LARGE_INTESTINE 102.852867 \n",
"geneExpression:PANC0213_PANCREAS 104.005952 \n",
"geneExpression:BXPC3_PANCREAS 102.885398 \n",
"geneExpression:SU8686_PANCREAS 104.132469 \n",
"geneExpression:SCC15_UPPER_AERODIGESTIVE_TRACT 102.905314 \n",
"geneExpression:CAPAN1_PANCREAS 103.968304 \n",
"geneExpression:CAL33_UPPER_AERODIGESTIVE_TRACT 103.469534 \n",
"geneExpression:SNU869_BILIARY_TRACT 104.341069 \n",
"geneExpression:SNU1076_UPPER_AERODIGESTIVE_TRACT 103.827220 \n",
"geneExpression:CAPAN2_PANCREAS 103.845722 \n",
"geneExpression:TCCPAN2_PANCREAS 102.811149 \n",
"geneExpression:BICR56_UPPER_AERODIGESTIVE_TRACT 104.257396 \n",
"geneExpression:SNU899_UPPER_AERODIGESTIVE_TRACT 103.499550 \n",
"geneExpression:BICR22_UPPER_AERODIGESTIVE_TRACT 104.241028 \n",
"geneExpression:CAL851_BREAST 103.913419 \n",
"geneExpression:SNU81_LARGE_INTESTINE 103.686087 \n",
"geneExpression:CAL27_UPPER_AERODIGESTIVE_TRACT 103.121752 \n",
"geneExpression:NCIH2444_LUNG 103.962997 \n",
"geneExpression:PANC0403_PANCREAS 104.189341 \n",
"geneExpression:JHUEM3_ENDOMETRIUM 104.154386 \n",
"geneExpression:KCIMOH1_PANCREAS 103.487881 \n",
"... ... \n",
"geneExpression:NCIH524_LUNG 113.287240 \n",
"geneExpression:NCIH82_LUNG 112.560303 \n",
"geneExpression:MOLT4_HAEMATOPOIETIC_AND_LYMPHOI... 107.661768 \n",
"geneExpression:OCILY10_HAEMATOPOIETIC_AND_LYMPH... 107.407158 \n",
"geneExpression:SKNBE2_AUTONOMIC_GANGLIA 113.237808 \n",
"geneExpression:NCIH69_LUNG 115.101682 \n",
"geneExpression:NCIH1436_LUNG 114.265589 \n",
"geneExpression:KELLY_AUTONOMIC_GANGLIA 112.966892 \n",
"geneExpression:PF382_HAEMATOPOIETIC_AND_LYMPHOI... 107.376778 \n",
"geneExpression:CA46_HAEMATOPOIETIC_AND_LYMPHOID... 106.611284 \n",
"geneExpression:SHSY5Y_AUTONOMIC_GANGLIA 113.851134 \n",
"geneExpression:CPCN_LUNG 113.580828 \n",
"geneExpression:NCIH2227_LUNG 114.848545 \n",
"geneExpression:BL70_HAEMATOPOIETIC_AND_LYMPHOID... 106.707253 \n",
"geneExpression:D341MED_CENTRAL_NERVOUS_SYSTEM 113.554310 \n",
"geneExpression:NCIH1930_LUNG 114.800850 \n",
"geneExpression:NCIH2081_LUNG 114.987104 \n",
"geneExpression:NCIH1963_LUNG 114.553522 \n",
"geneExpression:SKNDZ_AUTONOMIC_GANGLIA 113.516966 \n",
"geneExpression:KPNRTBM1_AUTONOMIC_GANGLIA 114.242117 \n",
"geneExpression:CORL24_LUNG 115.657538 \n",
"geneExpression:KPNYN_AUTONOMIC_GANGLIA 114.352648 \n",
"geneExpression:NCIH1694_LUNG 114.546258 \n",
"geneExpression:HCC33_LUNG 115.310846 \n",
"geneExpression:IMR32_AUTONOMIC_GANGLIA 113.925934 \n",
"geneExpression:CHP126_AUTONOMIC_GANGLIA 114.488787 \n",
"geneExpression:NCIH1184_LUNG 114.647574 \n",
"geneExpression:NCIH1105_LUNG 115.774789 \n",
"geneExpression:NCIH1092_LUNG 116.717420 \n",
"geneExpression:NCIH292_LUNG 155.154768 \n",
"\n",
"[1036 rows x 164 columns]"
]
},
"execution_count": 33,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"dist_matrix.sort_values(by=\"geneExpression:biosample:TCGA-PAAD:TCGA-2J-AAB4-01A\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"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": "2.7.12"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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