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ArcA expression data comparison to Park et al.
Raw
gistfile1.txt
{
"metadata": {
"name": ""
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"ArcA expression data comparison for Fig. S6"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"from trnlib.omeORM import *\n",
"from pandas import *\n",
"\n",
"from numpy import array\n",
"from sqlalchemy import func\n",
"\n",
"from IPython.core.display import HTML\n",
"\n",
"ome = Session()"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 88
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"s12 = read_table('S12_delta_arcA.txt', index_col='b number')"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 12
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"HTML(s12.to_html())"
],
"language": "python",
"metadata": {},
"outputs": [
{
"html": [
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>Strand</th>\n",
" <th>Operon</th>\n",
" <th>WT</th>\n",
" <th>\u0394arcA</th>\n",
" <th>Fold change</th>\n",
" <th>P value</th>\n",
" </tr>\n",
" <tr>\n",
" <th>b number</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>b0721</th>\n",
" <td> forward</td>\n",
" <td> sdhCDAB-sucABCD</td>\n",
" <td> 7.4</td>\n",
" <td> 14.4</td>\n",
" <td> 133.5</td>\n",
" <td> 5.450000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0432</th>\n",
" <td> reverse</td>\n",
" <td> cyoABCDE</td>\n",
" <td> 7.5</td>\n",
" <td> 13.5</td>\n",
" <td> 64.9</td>\n",
" <td> 5.550000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4069</th>\n",
" <td> reverse</td>\n",
" <td> acs-yjcH-actP</td>\n",
" <td> 6.1</td>\n",
" <td> 12.0</td>\n",
" <td> 57.5</td>\n",
" <td> 2.170000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1415</th>\n",
" <td> forward</td>\n",
" <td> aldA</td>\n",
" <td> 7.8</td>\n",
" <td> 13.0</td>\n",
" <td> 36.1</td>\n",
" <td> 9.620000e-08</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2210</th>\n",
" <td> reverse</td>\n",
" <td> mqo</td>\n",
" <td> 6.1</td>\n",
" <td> 11.1</td>\n",
" <td> 31.8</td>\n",
" <td> 7.290000e-08</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1014</th>\n",
" <td> reverse</td>\n",
" <td> putA</td>\n",
" <td> 5.9</td>\n",
" <td> 10.8</td>\n",
" <td> 30.8</td>\n",
" <td> 1.210000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2150</th>\n",
" <td> reverse</td>\n",
" <td> mglBAC</td>\n",
" <td> 5.5</td>\n",
" <td> 10.3</td>\n",
" <td> 29.2</td>\n",
" <td> 1.110000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3846</th>\n",
" <td> reverse</td>\n",
" <td> fadBA</td>\n",
" <td> 6.3</td>\n",
" <td> 11.0</td>\n",
" <td> 27.2</td>\n",
" <td> 3.040000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1612</th>\n",
" <td> reverse</td>\n",
" <td> fumA</td>\n",
" <td> 8.2</td>\n",
" <td> 12.9</td>\n",
" <td> 26.0</td>\n",
" <td> 2.030000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1020</th>\n",
" <td> forward</td>\n",
" <td> phoH</td>\n",
" <td> 5.5</td>\n",
" <td> 10.2</td>\n",
" <td> 25.3</td>\n",
" <td> 2.280000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0346</th>\n",
" <td> reverse</td>\n",
" <td> mhpR-lacI</td>\n",
" <td> 6.2</td>\n",
" <td> 10.8</td>\n",
" <td> 23.9</td>\n",
" <td> 1.430000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2310</th>\n",
" <td> reverse</td>\n",
" <td> argT-hisJQMP</td>\n",
" <td> 6.5</td>\n",
" <td> 11.0</td>\n",
" <td> 22.6</td>\n",
" <td> 2.280000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0598</th>\n",
" <td> forward</td>\n",
" <td> cstA</td>\n",
" <td> 7.3</td>\n",
" <td> 11.7</td>\n",
" <td> 21.5</td>\n",
" <td> 7.110000e-06</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0124</th>\n",
" <td> reverse</td>\n",
" <td> gcd</td>\n",
" <td> 6.8</td>\n",
" <td> 11.1</td>\n",
" <td> 20.0</td>\n",
" <td> 2.270000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3962</th>\n",
" <td> reverse</td>\n",
" <td> sthA</td>\n",
" <td> 7.5</td>\n",
" <td> 11.7</td>\n",
" <td> 18.3</td>\n",
" <td> 1.730000e-06</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0221</th>\n",
" <td> reverse</td>\n",
" <td> fadE</td>\n",
" <td> 6.3</td>\n",
" <td> 10.5</td>\n",
" <td> 17.5</td>\n",
" <td> 4.600000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1189</th>\n",
" <td> forward</td>\n",
" <td> dadAX</td>\n",
" <td> 8.7</td>\n",
" <td> 12.7</td>\n",
" <td> 16.0</td>\n",
" <td> 3.100000e-06</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1422</th>\n",
" <td> reverse</td>\n",
" <td> ydcI</td>\n",
" <td> 7.0</td>\n",
" <td> 11.0</td>\n",
" <td> 15.9</td>\n",
" <td> 3.730000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3820</th>\n",
" <td> reverse</td>\n",
" <td> yigI</td>\n",
" <td> 6.2</td>\n",
" <td> 10.1</td>\n",
" <td> 15.6</td>\n",
" <td> 5.480000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1297</th>\n",
" <td> reverse</td>\n",
" <td> puuA</td>\n",
" <td> 6.8</td>\n",
" <td> 10.7</td>\n",
" <td> 15.3</td>\n",
" <td> 2.740000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3528</th>\n",
" <td> reverse</td>\n",
" <td> dctA</td>\n",
" <td> 7.5</td>\n",
" <td> 11.5</td>\n",
" <td> 15.3</td>\n",
" <td> 5.750000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0118</th>\n",
" <td> forward</td>\n",
" <td> acnB</td>\n",
" <td> 9.6</td>\n",
" <td> 13.3</td>\n",
" <td> 13.7</td>\n",
" <td> 1.110000e-06</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2181</th>\n",
" <td> reverse</td>\n",
" <td> yejG</td>\n",
" <td> 7.4</td>\n",
" <td> 10.9</td>\n",
" <td> 11.9</td>\n",
" <td> 5.570000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1778</th>\n",
" <td> reverse</td>\n",
" <td> msrB</td>\n",
" <td> 9.2</td>\n",
" <td> 12.7</td>\n",
" <td> 11.6</td>\n",
" <td> 2.260000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1777</th>\n",
" <td> reverse</td>\n",
" <td> yeaC</td>\n",
" <td> 8.0</td>\n",
" <td> 11.5</td>\n",
" <td> 11.1</td>\n",
" <td> 8.080000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1748</th>\n",
" <td> reverse</td>\n",
" <td> astCADBE</td>\n",
" <td> 5.5</td>\n",
" <td> 8.9</td>\n",
" <td> 10.6</td>\n",
" <td> 5.510000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1298</th>\n",
" <td> forward</td>\n",
" <td> puuDR</td>\n",
" <td> 7.4</td>\n",
" <td> 10.8</td>\n",
" <td> 10.6</td>\n",
" <td> 5.540000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2342</th>\n",
" <td> reverse</td>\n",
" <td> fadIJ</td>\n",
" <td> 5.5</td>\n",
" <td> 8.8</td>\n",
" <td> 10.2</td>\n",
" <td> 5.460000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2980</th>\n",
" <td> forward</td>\n",
" <td> glcC</td>\n",
" <td> 5.7</td>\n",
" <td> 9.0</td>\n",
" <td> 9.8</td>\n",
" <td> 3.420000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1276</th>\n",
" <td> forward</td>\n",
" <td> acnA</td>\n",
" <td> 7.8</td>\n",
" <td> 11.0</td>\n",
" <td> 9.2</td>\n",
" <td> 1.550000e-06</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0450</th>\n",
" <td> forward</td>\n",
" <td> glnK-amtB</td>\n",
" <td> 5.2</td>\n",
" <td> 8.3</td>\n",
" <td> 8.8</td>\n",
" <td> 3.250000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2587</th>\n",
" <td> reverse</td>\n",
" <td> kgtP</td>\n",
" <td> 11.0</td>\n",
" <td> 14.2</td>\n",
" <td> 8.8</td>\n",
" <td> 3.620000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3236</th>\n",
" <td> reverse</td>\n",
" <td> mdh</td>\n",
" <td> 10.3</td>\n",
" <td> 13.5</td>\n",
" <td> 8.8</td>\n",
" <td> 1.510000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2586</th>\n",
" <td> forward</td>\n",
" <td> yfiM</td>\n",
" <td> 7.1</td>\n",
" <td> 10.2</td>\n",
" <td> 8.6</td>\n",
" <td> 1.280000e-06</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1611</th>\n",
" <td> reverse</td>\n",
" <td> fumC</td>\n",
" <td> 6.4</td>\n",
" <td> 9.5</td>\n",
" <td> 8.4</td>\n",
" <td> 2.190000e-06</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3605</th>\n",
" <td> forward</td>\n",
" <td> lldPRD</td>\n",
" <td> 6.6</td>\n",
" <td> 9.6</td>\n",
" <td> 8.3</td>\n",
" <td> 2.730000e-06</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2518</th>\n",
" <td> reverse</td>\n",
" <td> ndk</td>\n",
" <td> 9.2</td>\n",
" <td> 12.3</td>\n",
" <td> 8.2</td>\n",
" <td> 4.710000e-06</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3453</th>\n",
" <td> reverse</td>\n",
" <td> ugpBAECQ</td>\n",
" <td> 6.3</td>\n",
" <td> 9.3</td>\n",
" <td> 8.2</td>\n",
" <td> 2.950000e-06</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0458</th>\n",
" <td> reverse</td>\n",
" <td> ylaC</td>\n",
" <td> 6.1</td>\n",
" <td> 9.1</td>\n",
" <td> 7.7</td>\n",
" <td> 5.910000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4376</th>\n",
" <td> forward</td>\n",
" <td> osmY</td>\n",
" <td> 9.5</td>\n",
" <td> 12.4</td>\n",
" <td> 7.5</td>\n",
" <td> 3.650000e-06</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2979</th>\n",
" <td> reverse</td>\n",
" <td> glcDEFGBA</td>\n",
" <td> 6.4</td>\n",
" <td> 9.2</td>\n",
" <td> 7.1</td>\n",
" <td> 6.940000e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0720</th>\n",
" <td> reverse</td>\n",
" <td> gltA</td>\n",
" <td> 12.3</td>\n",
" <td> 15.1</td>\n",
" <td> 7.1</td>\n",
" <td> 9.660000e-06</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2537</th>\n",
" <td> reverse</td>\n",
" <td> hcaR</td>\n",
" <td> 6.8</td>\n",
" <td> 9.6</td>\n",
" <td> 6.8</td>\n",
" <td> 1.090000e-06</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0453</th>\n",
" <td> forward</td>\n",
" <td> ybaY</td>\n",
" <td> 7.3</td>\n",
" <td> 10.0</td>\n",
" <td> 6.4</td>\n",
" <td> 1.140000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1300</th>\n",
" <td> forward</td>\n",
" <td> puuCBE</td>\n",
" <td> 7.6</td>\n",
" <td> 10.3</td>\n",
" <td> 6.4</td>\n",
" <td> 3.370000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0116</th>\n",
" <td> forward</td>\n",
" <td> lpdA</td>\n",
" <td> 11.9</td>\n",
" <td> 14.5</td>\n",
" <td> 6.1</td>\n",
" <td> 1.100000e-06</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3894</th>\n",
" <td> reverse</td>\n",
" <td> fdoGHI-fdhE</td>\n",
" <td> 6.6</td>\n",
" <td> 9.2</td>\n",
" <td> 6.0</td>\n",
" <td> 8.850000e-06</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0314</th>\n",
" <td> forward</td>\n",
" <td> betT</td>\n",
" <td> 5.9</td>\n",
" <td> 8.5</td>\n",
" <td> 5.9</td>\n",
" <td> 4.670000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3160</th>\n",
" <td> forward</td>\n",
" <td> yhbW</td>\n",
" <td> 7.7</td>\n",
" <td> 10.2</td>\n",
" <td> 5.7</td>\n",
" <td> 5.560000e-06</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3073</th>\n",
" <td> forward</td>\n",
" <td> ygjG</td>\n",
" <td> 7.8</td>\n",
" <td> 10.3</td>\n",
" <td> 5.5</td>\n",
" <td> 4.750000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2111</th>\n",
" <td> reverse</td>\n",
" <td> yehDCBA</td>\n",
" <td> 6.5</td>\n",
" <td> 8.9</td>\n",
" <td> 5.4</td>\n",
" <td> 3.120000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0240</th>\n",
" <td> forward</td>\n",
" <td> crl</td>\n",
" <td> 9.8</td>\n",
" <td> 12.2</td>\n",
" <td> 5.2</td>\n",
" <td> 5.870000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2155</th>\n",
" <td> reverse</td>\n",
" <td> cirA</td>\n",
" <td> 6.5</td>\n",
" <td> 8.9</td>\n",
" <td> 5.2</td>\n",
" <td> 1.250000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2463</th>\n",
" <td> reverse</td>\n",
" <td> maeB</td>\n",
" <td> 8.3</td>\n",
" <td> 10.6</td>\n",
" <td> 4.9</td>\n",
" <td> 1.600000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4568</th>\n",
" <td> forward</td>\n",
" <td> ytjA</td>\n",
" <td> 8.5</td>\n",
" <td> 10.7</td>\n",
" <td> 4.7</td>\n",
" <td> 8.020000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1163</th>\n",
" <td> reverse</td>\n",
" <td> ycgF</td>\n",
" <td> 6.0</td>\n",
" <td> 8.2</td>\n",
" <td> 4.6</td>\n",
" <td> 5.530000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4519</th>\n",
" <td> forward</td>\n",
" <td> icdC</td>\n",
" <td> 7.3</td>\n",
" <td> 9.4</td>\n",
" <td> 4.4</td>\n",
" <td> 2.060000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0313</th>\n",
" <td> reverse</td>\n",
" <td> betIBA</td>\n",
" <td> 6.0</td>\n",
" <td> 8.1</td>\n",
" <td> 4.4</td>\n",
" <td> 5.200000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3819</th>\n",
" <td> reverse</td>\n",
" <td> rarD</td>\n",
" <td> 6.6</td>\n",
" <td> 8.7</td>\n",
" <td> 4.1</td>\n",
" <td> 1.500000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3128</th>\n",
" <td> forward</td>\n",
" <td> garD</td>\n",
" <td> 8.0</td>\n",
" <td> 10.0</td>\n",
" <td> 4.0</td>\n",
" <td> 3.940000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1136</th>\n",
" <td> forward</td>\n",
" <td> icdA</td>\n",
" <td> 13.0</td>\n",
" <td> 14.9</td>\n",
" <td> 4.0</td>\n",
" <td> 2.870000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0882</th>\n",
" <td> forward</td>\n",
" <td> clpA</td>\n",
" <td> 10.6</td>\n",
" <td> 12.5</td>\n",
" <td> 3.7</td>\n",
" <td> 3.910000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4034</th>\n",
" <td> reverse</td>\n",
" <td> malEFG</td>\n",
" <td> 8.7</td>\n",
" <td> 10.5</td>\n",
" <td> 3.4</td>\n",
" <td> 5.400000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1296</th>\n",
" <td> reverse</td>\n",
" <td> puuP</td>\n",
" <td> 6.2</td>\n",
" <td> 7.9</td>\n",
" <td> 3.4</td>\n",
" <td> 3.370000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1332</th>\n",
" <td> forward</td>\n",
" <td> ynaJ</td>\n",
" <td> 9.0</td>\n",
" <td> 10.7</td>\n",
" <td> 3.4</td>\n",
" <td> 4.410000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1256</th>\n",
" <td> forward</td>\n",
" <td> ompW</td>\n",
" <td> 8.1</td>\n",
" <td> 9.8</td>\n",
" <td> 3.3</td>\n",
" <td> 5.520000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3523</th>\n",
" <td> forward</td>\n",
" <td> yhjE</td>\n",
" <td> 10.5</td>\n",
" <td> 12.2</td>\n",
" <td> 3.2</td>\n",
" <td> 4.420000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1805</th>\n",
" <td> reverse</td>\n",
" <td> fadD-sroD</td>\n",
" <td> 7.0</td>\n",
" <td> 8.7</td>\n",
" <td> 3.2</td>\n",
" <td> 1.450000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0383</th>\n",
" <td> forward</td>\n",
" <td> phoA-psiF</td>\n",
" <td> 7.7</td>\n",
" <td> 9.4</td>\n",
" <td> 3.2</td>\n",
" <td> 2.930000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0836</th>\n",
" <td> forward</td>\n",
" <td> bssR</td>\n",
" <td> 10.7</td>\n",
" <td> 12.3</td>\n",
" <td> 3.2</td>\n",
" <td> 9.960000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0113</th>\n",
" <td> forward</td>\n",
" <td> pdhR-aceEF-lpd</td>\n",
" <td> 8.3</td>\n",
" <td> 9.9</td>\n",
" <td> 3.2</td>\n",
" <td> 2.120000e-02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2677</th>\n",
" <td> forward</td>\n",
" <td> proVWX</td>\n",
" <td> 5.8</td>\n",
" <td> 7.4</td>\n",
" <td> 3.1</td>\n",
" <td> 6.730000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2172</th>\n",
" <td> forward</td>\n",
" <td> yeiQ</td>\n",
" <td> 6.1</td>\n",
" <td> 7.8</td>\n",
" <td> 3.1</td>\n",
" <td> 2.050000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2844</th>\n",
" <td> reverse</td>\n",
" <td> yqeF</td>\n",
" <td> 6.0</td>\n",
" <td> 7.6</td>\n",
" <td> 3.1</td>\n",
" <td> 5.860000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3081</th>\n",
" <td> forward</td>\n",
" <td> fadH</td>\n",
" <td> 6.6</td>\n",
" <td> 8.2</td>\n",
" <td> 3.1</td>\n",
" <td> 1.280000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4490</th>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" <td> 5.9</td>\n",
" <td> 7.5</td>\n",
" <td> 3.1</td>\n",
" <td> 2.500000e-02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1040</th>\n",
" <td> reverse</td>\n",
" <td> csgDEFG</td>\n",
" <td> 8.0</td>\n",
" <td> 9.6</td>\n",
" <td> 3.0</td>\n",
" <td> 4.430000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0330</th>\n",
" <td> reverse</td>\n",
" <td> prpR</td>\n",
" <td> 6.1</td>\n",
" <td> 7.6</td>\n",
" <td> 2.9</td>\n",
" <td> 1.400000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4340</th>\n",
" <td> reverse</td>\n",
" <td> yjiR</td>\n",
" <td> 6.7</td>\n",
" <td> 8.2</td>\n",
" <td> 2.9</td>\n",
" <td> 2.110000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0031</th>\n",
" <td> forward</td>\n",
" <td> dapB</td>\n",
" <td> 9.9</td>\n",
" <td> 11.5</td>\n",
" <td> 2.9</td>\n",
" <td> 7.410000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3942</th>\n",
" <td> forward</td>\n",
" <td> katG</td>\n",
" <td> 12.6</td>\n",
" <td> 14.1</td>\n",
" <td> 2.9</td>\n",
" <td> 1.450000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0755</th>\n",
" <td> reverse</td>\n",
" <td> gpmA</td>\n",
" <td> 11.1</td>\n",
" <td> 12.6</td>\n",
" <td> 2.9</td>\n",
" <td> 7.440000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2344</th>\n",
" <td> forward</td>\n",
" <td> fadL</td>\n",
" <td> 7.3</td>\n",
" <td> 8.8</td>\n",
" <td> 2.8</td>\n",
" <td> 7.220000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3351</th>\n",
" <td> reverse</td>\n",
" <td> kefGB-yheV</td>\n",
" <td> 6.9</td>\n",
" <td> 8.4</td>\n",
" <td> 2.8</td>\n",
" <td> 3.830000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3995</th>\n",
" <td> reverse</td>\n",
" <td> rsd</td>\n",
" <td> 8.4</td>\n",
" <td> 10.0</td>\n",
" <td> 2.8</td>\n",
" <td> 1.300000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0655</th>\n",
" <td> reverse</td>\n",
" <td> gltI-sroC-gltJKL</td>\n",
" <td> 10.2</td>\n",
" <td> 11.7</td>\n",
" <td> 2.8</td>\n",
" <td> 9.180000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4014</th>\n",
" <td> forward</td>\n",
" <td> aceBAK</td>\n",
" <td> 13.1</td>\n",
" <td> 14.6</td>\n",
" <td> 2.8</td>\n",
" <td> 9.940000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3403</th>\n",
" <td> forward</td>\n",
" <td> pck</td>\n",
" <td> 10.4</td>\n",
" <td> 11.9</td>\n",
" <td> 2.8</td>\n",
" <td> 1.010000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1021</th>\n",
" <td> reverse</td>\n",
" <td> pgaABCD</td>\n",
" <td> 6.3</td>\n",
" <td> 7.8</td>\n",
" <td> 2.7</td>\n",
" <td> 4.970000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0584</th>\n",
" <td> reverse</td>\n",
" <td> fepA-entD</td>\n",
" <td> 6.4</td>\n",
" <td> 7.8</td>\n",
" <td> 2.7</td>\n",
" <td> 4.120000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2287</th>\n",
" <td> reverse</td>\n",
" <td> nuoABCEFGHIJKLMN</td>\n",
" <td> 11.8</td>\n",
" <td> 13.3</td>\n",
" <td> 2.7</td>\n",
" <td> 8.390000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1674</th>\n",
" <td> reverse</td>\n",
" <td> ydhYVWXUT</td>\n",
" <td> 8.4</td>\n",
" <td> 9.9</td>\n",
" <td> 2.7</td>\n",
" <td> 1.290000e-02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0628</th>\n",
" <td> reverse</td>\n",
" <td> lipA</td>\n",
" <td> 11.0</td>\n",
" <td> 12.4</td>\n",
" <td> 2.7</td>\n",
" <td> 9.560000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2582</th>\n",
" <td> forward</td>\n",
" <td> trxC</td>\n",
" <td> 6.7</td>\n",
" <td> 8.1</td>\n",
" <td> 2.7</td>\n",
" <td> 4.050000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1452</th>\n",
" <td> forward</td>\n",
" <td> yncE</td>\n",
" <td> 7.0</td>\n",
" <td> 8.4</td>\n",
" <td> 2.6</td>\n",
" <td> 2.910000e-02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4035</th>\n",
" <td> forward</td>\n",
" <td> malK-lamB-malM</td>\n",
" <td> 6.4</td>\n",
" <td> 7.8</td>\n",
" <td> 2.6</td>\n",
" <td> 8.780000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0306</th>\n",
" <td> forward</td>\n",
" <td> ykgEFG</td>\n",
" <td> 6.7</td>\n",
" <td> 8.0</td>\n",
" <td> 2.6</td>\n",
" <td> 8.330000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1534</th>\n",
" <td> forward</td>\n",
" <td> ydeE</td>\n",
" <td> 6.6</td>\n",
" <td> 8.0</td>\n",
" <td> 2.6</td>\n",
" <td> 3.280000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3397</th>\n",
" <td> reverse</td>\n",
" <td> nudE</td>\n",
" <td> 6.5</td>\n",
" <td> 7.9</td>\n",
" <td> 2.6</td>\n",
" <td> 1.700000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0854</th>\n",
" <td> forward</td>\n",
" <td> potFGHI</td>\n",
" <td> 11.3</td>\n",
" <td> 12.6</td>\n",
" <td> 2.6</td>\n",
" <td> 5.760000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2574</th>\n",
" <td> forward</td>\n",
" <td> nadB</td>\n",
" <td> 10.6</td>\n",
" <td> 12.0</td>\n",
" <td> 2.6</td>\n",
" <td> 1.690000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2152</th>\n",
" <td> reverse</td>\n",
" <td> folE-yeiB</td>\n",
" <td> 7.9</td>\n",
" <td> 9.2</td>\n",
" <td> 2.5</td>\n",
" <td> 2.120000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3751</th>\n",
" <td> forward</td>\n",
" <td> rbsDACBKR</td>\n",
" <td> 9.8</td>\n",
" <td> 11.2</td>\n",
" <td> 2.5</td>\n",
" <td> 3.370000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1451</th>\n",
" <td> reverse</td>\n",
" <td> yncD</td>\n",
" <td> 6.8</td>\n",
" <td> 8.1</td>\n",
" <td> 2.5</td>\n",
" <td> 6.000000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0821</th>\n",
" <td> reverse</td>\n",
" <td> ybiU</td>\n",
" <td> 5.9</td>\n",
" <td> 7.2</td>\n",
" <td> 2.4</td>\n",
" <td> 1.440000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4512</th>\n",
" <td> forward</td>\n",
" <td> ybdD</td>\n",
" <td> 7.2</td>\n",
" <td> 8.4</td>\n",
" <td> 2.4</td>\n",
" <td> 9.910000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2392</th>\n",
" <td> reverse</td>\n",
" <td> mntH</td>\n",
" <td> 8.3</td>\n",
" <td> 9.6</td>\n",
" <td> 2.4</td>\n",
" <td> 2.410000e-02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0608</th>\n",
" <td> forward</td>\n",
" <td> ybdR</td>\n",
" <td> 8.6</td>\n",
" <td> 9.9</td>\n",
" <td> 2.4</td>\n",
" <td> 7.830000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1164</th>\n",
" <td> forward</td>\n",
" <td> ycgZ-ymgA-ariR-ymgC</td>\n",
" <td> 5.6</td>\n",
" <td> 6.9</td>\n",
" <td> 2.4</td>\n",
" <td> 4.880000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3795</th>\n",
" <td> forward</td>\n",
" <td> yifK</td>\n",
" <td> 10.1</td>\n",
" <td> 11.3</td>\n",
" <td> 2.4</td>\n",
" <td> 1.330000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1015</th>\n",
" <td> forward</td>\n",
" <td> putP</td>\n",
" <td> 9.9</td>\n",
" <td> 11.1</td>\n",
" <td> 2.4</td>\n",
" <td> 4.930000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3268</th>\n",
" <td> forward</td>\n",
" <td> yhdWXYZ</td>\n",
" <td> 6.7</td>\n",
" <td> 7.9</td>\n",
" <td> 2.3</td>\n",
" <td> 3.470000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1702</th>\n",
" <td> reverse</td>\n",
" <td> ppsA</td>\n",
" <td> 9.1</td>\n",
" <td> 10.3</td>\n",
" <td> 2.3</td>\n",
" <td> 2.750000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3324</th>\n",
" <td> forward</td>\n",
" <td> gspCDEFGHIJKLMO</td>\n",
" <td> 6.6</td>\n",
" <td> 7.8</td>\n",
" <td> 2.3</td>\n",
" <td> 9.880000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1444</th>\n",
" <td> forward</td>\n",
" <td> ydcW</td>\n",
" <td> 7.9</td>\n",
" <td> 9.2</td>\n",
" <td> 2.3</td>\n",
" <td> 2.430000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0452</th>\n",
" <td> reverse</td>\n",
" <td> tesB</td>\n",
" <td> 8.5</td>\n",
" <td> 9.7</td>\n",
" <td> 2.3</td>\n",
" <td> 7.600000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4139</th>\n",
" <td> reverse</td>\n",
" <td> aspA</td>\n",
" <td> 9.2</td>\n",
" <td> 10.4</td>\n",
" <td> 2.3</td>\n",
" <td> 3.260000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1765</th>\n",
" <td> reverse</td>\n",
" <td> ydjA-selD-topB</td>\n",
" <td> 11.2</td>\n",
" <td> 12.3</td>\n",
" <td> 2.2</td>\n",
" <td> 2.270000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0593</th>\n",
" <td> forward</td>\n",
" <td> entCEBAH</td>\n",
" <td> 6.5</td>\n",
" <td> 7.7</td>\n",
" <td> 2.2</td>\n",
" <td> 1.660000e-02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3592</th>\n",
" <td> reverse</td>\n",
" <td> yibF</td>\n",
" <td> 7.5</td>\n",
" <td> 8.7</td>\n",
" <td> 2.2</td>\n",
" <td> 5.940000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1536</th>\n",
" <td> reverse</td>\n",
" <td> ydeI</td>\n",
" <td> 7.2</td>\n",
" <td> 8.4</td>\n",
" <td> 2.2</td>\n",
" <td> 1.500000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2209</th>\n",
" <td> forward</td>\n",
" <td> eco</td>\n",
" <td> 9.0</td>\n",
" <td> 10.2</td>\n",
" <td> 2.2</td>\n",
" <td> 1.500000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0527</th>\n",
" <td> reverse</td>\n",
" <td> ybcI</td>\n",
" <td> 8.2</td>\n",
" <td> 9.3</td>\n",
" <td> 2.2</td>\n",
" <td> 2.060000e-02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0382</th>\n",
" <td> forward</td>\n",
" <td> iraP</td>\n",
" <td> 9.8</td>\n",
" <td> 11.0</td>\n",
" <td> 2.2</td>\n",
" <td> 1.860000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3744</th>\n",
" <td> forward</td>\n",
" <td> asnA</td>\n",
" <td> 8.1</td>\n",
" <td> 9.2</td>\n",
" <td> 2.2</td>\n",
" <td> 7.070000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3616</th>\n",
" <td> reverse</td>\n",
" <td> kbl-tdh</td>\n",
" <td> 9.4</td>\n",
" <td> 10.5</td>\n",
" <td> 2.1</td>\n",
" <td> 9.870000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1384</th>\n",
" <td> reverse</td>\n",
" <td> feaR</td>\n",
" <td> 5.9</td>\n",
" <td> 7.0</td>\n",
" <td> 2.1</td>\n",
" <td> 2.380000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0319</th>\n",
" <td> forward</td>\n",
" <td> yahDEFG</td>\n",
" <td> 5.7</td>\n",
" <td> 6.8</td>\n",
" <td> 2.1</td>\n",
" <td> 3.360000e-02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0304</th>\n",
" <td> reverse</td>\n",
" <td> ykgC</td>\n",
" <td> 8.3</td>\n",
" <td> 9.4</td>\n",
" <td> 2.1</td>\n",
" <td> 6.980000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3662</th>\n",
" <td> reverse</td>\n",
" <td> nepI</td>\n",
" <td> 7.0</td>\n",
" <td> 8.1</td>\n",
" <td> 2.1</td>\n",
" <td> 2.880000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0443</th>\n",
" <td> forward</td>\n",
" <td> fadM</td>\n",
" <td> 6.8</td>\n",
" <td> 7.9</td>\n",
" <td> 2.1</td>\n",
" <td> 3.820000e-02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1761</th>\n",
" <td> forward</td>\n",
" <td> gdhA</td>\n",
" <td> 13.4</td>\n",
" <td> 14.5</td>\n",
" <td> 2.1</td>\n",
" <td> 8.070000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0286</th>\n",
" <td> reverse</td>\n",
" <td> yagTSRQ</td>\n",
" <td> 5.7</td>\n",
" <td> 6.8</td>\n",
" <td> 2.1</td>\n",
" <td> 1.250000e-02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0356</th>\n",
" <td> reverse</td>\n",
" <td> frmRAB</td>\n",
" <td> 9.4</td>\n",
" <td> 10.4</td>\n",
" <td> 2.1</td>\n",
" <td> 4.820000e-02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1607</th>\n",
" <td> reverse</td>\n",
" <td> ydgC</td>\n",
" <td> 7.9</td>\n",
" <td> 8.9</td>\n",
" <td> 2.0</td>\n",
" <td> 2.040000e-02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1533</th>\n",
" <td> reverse</td>\n",
" <td> eamA</td>\n",
" <td> 9.7</td>\n",
" <td> 10.7</td>\n",
" <td> 2.0</td>\n",
" <td> 2.070000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1197</th>\n",
" <td> reverse</td>\n",
" <td> treA</td>\n",
" <td> 10.2</td>\n",
" <td> 11.2</td>\n",
" <td> 2.0</td>\n",
" <td> 9.770000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2876</th>\n",
" <td> reverse</td>\n",
" <td> yqeC</td>\n",
" <td> 6.4</td>\n",
" <td> 7.4</td>\n",
" <td> 2.0</td>\n",
" <td> 8.070000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2133</th>\n",
" <td> forward</td>\n",
" <td> dld</td>\n",
" <td> 10.4</td>\n",
" <td> 11.4</td>\n",
" <td> 2.0</td>\n",
" <td> 2.830000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0020</th>\n",
" <td> forward</td>\n",
" <td> nhaAR</td>\n",
" <td> 8.1</td>\n",
" <td> 7.1</td>\n",
" <td> -2.0</td>\n",
" <td> 8.410000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4280</th>\n",
" <td> forward</td>\n",
" <td> yjhBC</td>\n",
" <td> 9.2</td>\n",
" <td> 8.2</td>\n",
" <td> -2.0</td>\n",
" <td> 8.200000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1826</th>\n",
" <td> reverse</td>\n",
" <td> mgrB</td>\n",
" <td> 10.8</td>\n",
" <td> 9.8</td>\n",
" <td> -2.0</td>\n",
" <td> 4.110000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1223</th>\n",
" <td> forward</td>\n",
" <td> narK</td>\n",
" <td> 10.8</td>\n",
" <td> 9.8</td>\n",
" <td> -2.0</td>\n",
" <td> 1.520000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2690</th>\n",
" <td> reverse</td>\n",
" <td> yqaBA</td>\n",
" <td> 10.1</td>\n",
" <td> 9.1</td>\n",
" <td> -2.0</td>\n",
" <td> 4.430000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1251</th>\n",
" <td> reverse</td>\n",
" <td> yciI</td>\n",
" <td> 10.2</td>\n",
" <td> 9.2</td>\n",
" <td> -2.0</td>\n",
" <td> 7.800000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2419</th>\n",
" <td> forward</td>\n",
" <td> yfeKS</td>\n",
" <td> 7.2</td>\n",
" <td> 6.2</td>\n",
" <td> -2.0</td>\n",
" <td> 4.410000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1623</th>\n",
" <td> forward</td>\n",
" <td> add</td>\n",
" <td> 9.3</td>\n",
" <td> 8.2</td>\n",
" <td> -2.0</td>\n",
" <td> 2.970000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3042</th>\n",
" <td> forward</td>\n",
" <td> yqiC</td>\n",
" <td> 10.8</td>\n",
" <td> 9.8</td>\n",
" <td> -2.0</td>\n",
" <td> 9.210000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4598</th>\n",
" <td> reverse</td>\n",
" <td> yncL</td>\n",
" <td> 10.8</td>\n",
" <td> 9.7</td>\n",
" <td> -2.0</td>\n",
" <td> 1.110000e-02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0034</th>\n",
" <td> forward</td>\n",
" <td> caiF</td>\n",
" <td> 11.2</td>\n",
" <td> 10.2</td>\n",
" <td> -2.0</td>\n",
" <td> 9.180000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2350</th>\n",
" <td> forward</td>\n",
" <td> yfdGHI</td>\n",
" <td> 12.4</td>\n",
" <td> 11.3</td>\n",
" <td> -2.1</td>\n",
" <td> 1.850000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1243</th>\n",
" <td> forward</td>\n",
" <td> oppABCDF</td>\n",
" <td> 15.2</td>\n",
" <td> 14.2</td>\n",
" <td> -2.1</td>\n",
" <td> 1.570000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4057</th>\n",
" <td> forward</td>\n",
" <td> yjbQR</td>\n",
" <td> 10.4</td>\n",
" <td> 9.3</td>\n",
" <td> -2.1</td>\n",
" <td> 4.440000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0211</th>\n",
" <td> reverse</td>\n",
" <td> mltD</td>\n",
" <td> 10.0</td>\n",
" <td> 9.0</td>\n",
" <td> -2.1</td>\n",
" <td> 3.720000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0189</th>\n",
" <td> reverse</td>\n",
" <td> yaeP-rof</td>\n",
" <td> 7.8</td>\n",
" <td> 6.7</td>\n",
" <td> -2.1</td>\n",
" <td> 3.720000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3103</th>\n",
" <td> forward</td>\n",
" <td> yhaH</td>\n",
" <td> 9.5</td>\n",
" <td> 8.5</td>\n",
" <td> -2.1</td>\n",
" <td> 2.760000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2346</th>\n",
" <td> forward</td>\n",
" <td> mlaA</td>\n",
" <td> 9.5</td>\n",
" <td> 8.4</td>\n",
" <td> -2.1</td>\n",
" <td> 6.180000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3865</th>\n",
" <td> reverse</td>\n",
" <td> yihA</td>\n",
" <td> 8.1</td>\n",
" <td> 7.1</td>\n",
" <td> -2.1</td>\n",
" <td> 1.290000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2617</th>\n",
" <td> forward</td>\n",
" <td> smpA</td>\n",
" <td> 8.5</td>\n",
" <td> 7.4</td>\n",
" <td> -2.1</td>\n",
" <td> 1.010000e-02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3028</th>\n",
" <td> forward</td>\n",
" <td> mdaB</td>\n",
" <td> 9.5</td>\n",
" <td> 8.4</td>\n",
" <td> -2.1</td>\n",
" <td> 6.690000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2351</th>\n",
" <td> forward</td>\n",
" <td> yfdGHI</td>\n",
" <td> 12.4</td>\n",
" <td> 11.3</td>\n",
" <td> -2.1</td>\n",
" <td> 4.450000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1874</th>\n",
" <td> reverse</td>\n",
" <td> cutC</td>\n",
" <td> 8.5</td>\n",
" <td> 7.4</td>\n",
" <td> -2.2</td>\n",
" <td> 3.420000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3466</th>\n",
" <td> forward</td>\n",
" <td> rsmD-yhhL</td>\n",
" <td> 7.5</td>\n",
" <td> 6.4</td>\n",
" <td> -2.2</td>\n",
" <td> 6.990000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3343</th>\n",
" <td> reverse</td>\n",
" <td> yheONML</td>\n",
" <td> 8.0</td>\n",
" <td> 6.8</td>\n",
" <td> -2.2</td>\n",
" <td> 9.770000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3023</th>\n",
" <td> reverse</td>\n",
" <td> ygiV</td>\n",
" <td> 8.4</td>\n",
" <td> 7.3</td>\n",
" <td> -2.2</td>\n",
" <td> 1.130000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2175</th>\n",
" <td> forward</td>\n",
" <td> spr</td>\n",
" <td> 9.1</td>\n",
" <td> 8.0</td>\n",
" <td> -2.2</td>\n",
" <td> 5.590000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3494</th>\n",
" <td> reverse</td>\n",
" <td> uspB</td>\n",
" <td> 9.6</td>\n",
" <td> 8.4</td>\n",
" <td> -2.2</td>\n",
" <td> 1.030000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1792</th>\n",
" <td> forward</td>\n",
" <td> yeaO</td>\n",
" <td> 9.2</td>\n",
" <td> 8.1</td>\n",
" <td> -2.2</td>\n",
" <td> 3.870000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0075</th>\n",
" <td> reverse</td>\n",
" <td> leuLABCD</td>\n",
" <td> 9.7</td>\n",
" <td> 8.6</td>\n",
" <td> -2.2</td>\n",
" <td> 8.990000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4117</th>\n",
" <td> reverse</td>\n",
" <td> adiA</td>\n",
" <td> 7.1</td>\n",
" <td> 6.0</td>\n",
" <td> -2.2</td>\n",
" <td> 5.510000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1869</th>\n",
" <td> forward</td>\n",
" <td> yecN-cmoAB</td>\n",
" <td> 10.0</td>\n",
" <td> 8.8</td>\n",
" <td> -2.2</td>\n",
" <td> 9.230000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0961</th>\n",
" <td> reverse</td>\n",
" <td> yccFS</td>\n",
" <td> 11.4</td>\n",
" <td> 10.3</td>\n",
" <td> -2.2</td>\n",
" <td> 3.250000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4595</th>\n",
" <td> forward</td>\n",
" <td> yciY</td>\n",
" <td> 7.8</td>\n",
" <td> 6.6</td>\n",
" <td> -2.2</td>\n",
" <td> 4.150000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1250</th>\n",
" <td> reverse</td>\n",
" <td> kch</td>\n",
" <td> 9.3</td>\n",
" <td> 8.1</td>\n",
" <td> -2.3</td>\n",
" <td> 4.430000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2796</th>\n",
" <td> forward</td>\n",
" <td> sdaCB</td>\n",
" <td> 8.5</td>\n",
" <td> 7.2</td>\n",
" <td> -2.3</td>\n",
" <td> 4.720000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4640</th>\n",
" <td> reverse</td>\n",
" <td> upp-uraA</td>\n",
" <td> 8.0</td>\n",
" <td> 6.8</td>\n",
" <td> -2.3</td>\n",
" <td> 5.030000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1626</th>\n",
" <td> forward</td>\n",
" <td> ydgK-rsxABCDGE-nth</td>\n",
" <td> 9.6</td>\n",
" <td> 8.3</td>\n",
" <td> -2.3</td>\n",
" <td> 2.260000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1825</th>\n",
" <td> reverse</td>\n",
" <td> yebO</td>\n",
" <td> 8.3</td>\n",
" <td> 7.1</td>\n",
" <td> -2.3</td>\n",
" <td> 5.760000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1273</th>\n",
" <td> reverse</td>\n",
" <td> yciN</td>\n",
" <td> 9.6</td>\n",
" <td> 8.3</td>\n",
" <td> -2.4</td>\n",
" <td> 1.730000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4606</th>\n",
" <td> reverse</td>\n",
" <td> ypfM</td>\n",
" <td> 7.0</td>\n",
" <td> 5.8</td>\n",
" <td> -2.4</td>\n",
" <td> 1.110000e-02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0485</th>\n",
" <td> forward</td>\n",
" <td> ybaST</td>\n",
" <td> 12.0</td>\n",
" <td> 10.8</td>\n",
" <td> -2.4</td>\n",
" <td> 2.440000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1224</th>\n",
" <td> forward</td>\n",
" <td> narGHJI</td>\n",
" <td> 11.6</td>\n",
" <td> 10.3</td>\n",
" <td> -2.4</td>\n",
" <td> 8.080000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1000</th>\n",
" <td> reverse</td>\n",
" <td> cbpAM</td>\n",
" <td> 12.3</td>\n",
" <td> 11.0</td>\n",
" <td> -2.4</td>\n",
" <td> 5.680000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0704</th>\n",
" <td> forward</td>\n",
" <td> ybfOC</td>\n",
" <td> 7.3</td>\n",
" <td> 6.0</td>\n",
" <td> -2.4</td>\n",
" <td> 4.690000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0762</th>\n",
" <td> forward</td>\n",
" <td> ybhT</td>\n",
" <td> 8.4</td>\n",
" <td> 7.1</td>\n",
" <td> -2.5</td>\n",
" <td> 1.140000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1054</th>\n",
" <td> reverse</td>\n",
" <td> lpxL</td>\n",
" <td> 10.4</td>\n",
" <td> 9.1</td>\n",
" <td> -2.5</td>\n",
" <td> 5.850000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0001</th>\n",
" <td> forward</td>\n",
" <td> thrLABC</td>\n",
" <td> 12.7</td>\n",
" <td> 11.4</td>\n",
" <td> -2.5</td>\n",
" <td> 6.510000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0968</th>\n",
" <td> forward</td>\n",
" <td> yccX</td>\n",
" <td> 7.9</td>\n",
" <td> 6.6</td>\n",
" <td> -2.5</td>\n",
" <td> 3.860000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1143</th>\n",
" <td> forward</td>\n",
" <td> ymfI</td>\n",
" <td> 9.5</td>\n",
" <td> 8.2</td>\n",
" <td> -2.5</td>\n",
" <td> 1.820000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4046</th>\n",
" <td> reverse</td>\n",
" <td> zur</td>\n",
" <td> 8.5</td>\n",
" <td> 7.2</td>\n",
" <td> -2.5</td>\n",
" <td> 6.490000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1634</th>\n",
" <td> forward</td>\n",
" <td> tppB</td>\n",
" <td> 9.1</td>\n",
" <td> 7.8</td>\n",
" <td> -2.5</td>\n",
" <td> 6.140000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4402</th>\n",
" <td> NaN</td>\n",
" <td> yjjY</td>\n",
" <td> 13.2</td>\n",
" <td> 11.8</td>\n",
" <td> -2.6</td>\n",
" <td> 3.650000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1974</th>\n",
" <td> forward</td>\n",
" <td> yodB</td>\n",
" <td> 8.9</td>\n",
" <td> 7.5</td>\n",
" <td> -2.6</td>\n",
" <td> 2.240000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0833</th>\n",
" <td> forward</td>\n",
" <td> yliEF</td>\n",
" <td> 7.8</td>\n",
" <td> 6.4</td>\n",
" <td> -2.6</td>\n",
" <td> 3.300000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0559</th>\n",
" <td> reverse</td>\n",
" <td> ybcW</td>\n",
" <td> 7.0</td>\n",
" <td> 5.6</td>\n",
" <td> -2.6</td>\n",
" <td> 2.460000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1185</th>\n",
" <td> reverse</td>\n",
" <td> dsbB</td>\n",
" <td> 8.3</td>\n",
" <td> 6.9</td>\n",
" <td> -2.7</td>\n",
" <td> 1.280000e-02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4641</th>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" <td> 8.3</td>\n",
" <td> 6.9</td>\n",
" <td> -2.7</td>\n",
" <td> 4.590000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4377</th>\n",
" <td> forward</td>\n",
" <td> yjjUV</td>\n",
" <td> 10.4</td>\n",
" <td> 8.9</td>\n",
" <td> -2.8</td>\n",
" <td> 1.270000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4589</th>\n",
" <td> reverse</td>\n",
" <td> ylcI</td>\n",
" <td> 8.8</td>\n",
" <td> 7.3</td>\n",
" <td> -2.8</td>\n",
" <td> 5.370000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0622</th>\n",
" <td> forward</td>\n",
" <td> pagP</td>\n",
" <td> 7.8</td>\n",
" <td> 6.3</td>\n",
" <td> -2.8</td>\n",
" <td> 9.290000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3510</th>\n",
" <td> reverse</td>\n",
" <td> hdeAB-yhiD</td>\n",
" <td> 15.0</td>\n",
" <td> 13.4</td>\n",
" <td> -2.9</td>\n",
" <td> 1.530000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1073</th>\n",
" <td> forward</td>\n",
" <td> flgBCDEFGHIJ</td>\n",
" <td> 7.3</td>\n",
" <td> 5.8</td>\n",
" <td> -2.9</td>\n",
" <td> 1.650000e-02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2290</th>\n",
" <td> forward</td>\n",
" <td> yfbQ</td>\n",
" <td> 10.8</td>\n",
" <td> 9.2</td>\n",
" <td> -2.9</td>\n",
" <td> 3.580000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4187</th>\n",
" <td> forward</td>\n",
" <td> aidB</td>\n",
" <td> 10.4</td>\n",
" <td> 8.8</td>\n",
" <td> -3.0</td>\n",
" <td> 1.180000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3071</th>\n",
" <td> forward</td>\n",
" <td> yqjI</td>\n",
" <td> 10.0</td>\n",
" <td> 8.4</td>\n",
" <td> -3.0</td>\n",
" <td> 5.830000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4077</th>\n",
" <td> forward</td>\n",
" <td> gltP</td>\n",
" <td> 9.2</td>\n",
" <td> 7.6</td>\n",
" <td> -3.0</td>\n",
" <td> 1.740000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3516</th>\n",
" <td> reverse</td>\n",
" <td> gadXW</td>\n",
" <td> 11.3</td>\n",
" <td> 9.6</td>\n",
" <td> -3.1</td>\n",
" <td> 1.910000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0699</th>\n",
" <td> forward</td>\n",
" <td> ybfA</td>\n",
" <td> 7.3</td>\n",
" <td> 5.7</td>\n",
" <td> -3.2</td>\n",
" <td> 8.610000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1923</th>\n",
" <td> reverse</td>\n",
" <td> fliC</td>\n",
" <td> 8.3</td>\n",
" <td> 6.5</td>\n",
" <td> -3.6</td>\n",
" <td> 1.000000e-02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0972</th>\n",
" <td> forward</td>\n",
" <td> hyaABCDEF</td>\n",
" <td> 14.0</td>\n",
" <td> 12.1</td>\n",
" <td> -3.7</td>\n",
" <td> 1.750000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3408</th>\n",
" <td> forward</td>\n",
" <td> feoABC</td>\n",
" <td> 9.4</td>\n",
" <td> 7.5</td>\n",
" <td> -3.7</td>\n",
" <td> 6.000000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2847</th>\n",
" <td> forward</td>\n",
" <td> yqeIJ</td>\n",
" <td> 8.5</td>\n",
" <td> 6.6</td>\n",
" <td> -3.8</td>\n",
" <td> 3.370000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3506</th>\n",
" <td> forward</td>\n",
" <td> slp-dctR</td>\n",
" <td> 12.7</td>\n",
" <td> 10.7</td>\n",
" <td> -4.0</td>\n",
" <td> 1.360000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4409</th>\n",
" <td> forward</td>\n",
" <td> blr</td>\n",
" <td> 9.9</td>\n",
" <td> 7.9</td>\n",
" <td> -4.1</td>\n",
" <td> 8.640000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0621</th>\n",
" <td> reverse</td>\n",
" <td> dcuC</td>\n",
" <td> 9.2</td>\n",
" <td> 7.1</td>\n",
" <td> -4.1</td>\n",
" <td> 4.680000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0978</th>\n",
" <td> forward</td>\n",
" <td> appCB-yccB-appA</td>\n",
" <td> 12.5</td>\n",
" <td> 10.4</td>\n",
" <td> -4.1</td>\n",
" <td> 1.070000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3511</th>\n",
" <td> forward</td>\n",
" <td> hdeD</td>\n",
" <td> 14.7</td>\n",
" <td> 12.7</td>\n",
" <td> -4.2</td>\n",
" <td> 4.160000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1493</th>\n",
" <td> reverse</td>\n",
" <td> gadBC</td>\n",
" <td> 13.3</td>\n",
" <td> 11.2</td>\n",
" <td> -4.2</td>\n",
" <td> 3.710000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0564</th>\n",
" <td> forward</td>\n",
" <td> appY</td>\n",
" <td> 8.8</td>\n",
" <td> 6.5</td>\n",
" <td> -4.6</td>\n",
" <td> 2.930000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3517</th>\n",
" <td> reverse</td>\n",
" <td> gadAXW</td>\n",
" <td> 12.9</td>\n",
" <td> 10.7</td>\n",
" <td> -4.8</td>\n",
" <td> 1.700000e-03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2669</th>\n",
" <td> reverse</td>\n",
" <td> stpA</td>\n",
" <td> 11.1</td>\n",
" <td> 8.7</td>\n",
" <td> -5.2</td>\n",
" <td> 3.050000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1172</th>\n",
" <td> reverse</td>\n",
" <td> ymgGD</td>\n",
" <td> 10.0</td>\n",
" <td> 7.6</td>\n",
" <td> -5.4</td>\n",
" <td> 4.590000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4354</th>\n",
" <td> reverse</td>\n",
" <td> yjiY</td>\n",
" <td> 8.6</td>\n",
" <td> 6.0</td>\n",
" <td> -6.2</td>\n",
" <td> 1.130000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1625</th>\n",
" <td> forward</td>\n",
" <td> cnu</td>\n",
" <td> 10.1</td>\n",
" <td> 7.5</td>\n",
" <td> -6.4</td>\n",
" <td> 1.060000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0848</th>\n",
" <td> forward</td>\n",
" <td> ybjM</td>\n",
" <td> 8.9</td>\n",
" <td> 6.2</td>\n",
" <td> -6.4</td>\n",
" <td> 5.430000e-06</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4116</th>\n",
" <td> reverse</td>\n",
" <td> adiY</td>\n",
" <td> 10.4</td>\n",
" <td> 7.6</td>\n",
" <td> -6.9</td>\n",
" <td> 1.930000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4115</th>\n",
" <td> reverse</td>\n",
" <td> adiC</td>\n",
" <td> 9.3</td>\n",
" <td> 6.3</td>\n",
" <td> -8.0</td>\n",
" <td> 4.790000e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3512</th>\n",
" <td> forward</td>\n",
" <td> gadE-mdtEF</td>\n",
" <td> 12.4</td>\n",
" <td> 8.8</td>\n",
" <td> -11.4</td>\n",
" <td> 2.440000e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3491</th>\n",
" <td> forward</td>\n",
" <td> yhiM</td>\n",
" <td> 10.2</td>\n",
" <td> 6.3</td>\n",
" <td> -15.0</td>\n",
" <td> 8.150000e-06</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>"
],
"metadata": {},
"output_type": "pyout",
"prompt_number": 11,
"text": [
"<IPython.core.display.HTML at 0x10396cd10>"
]
}
],
"prompt_number": 11
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"aa = AllAnalysis\n",
"ome.query(aa).filter(and_(or_(aa.target1 == 'delta-arcA', aa.target2 == 'delta-arcA'),\\\n",
" or_(aa.target1 == 'wt', aa.target2 == 'wt'), aa.bnum == 'b1611',\\\n",
" aa.eacceptor1 == 'anaerobic')).all()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 6,
"text": [
"[]"
]
}
],
"prompt_number": 6
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"aa = AllAnalysis\n",
"ome.query(aa).filter(and_(or_(aa.target1 == 'delta-arcA', aa.target2 == 'delta-arcA'),\\\n",
" or_(aa.target1 == 'wt', aa.target2 == 'wt'), aa.fdr < .05, aa.gene_name.ilike('yfb%'),\\\n",
" or_(and_(aa.eacceptor1 == 'anaerobic', aa.eacceptor2 == 'anaerobic'),\\\n",
" and_(aa.eacceptor1 == 'NO3', aa.eacceptor2 == 'NO3'),\\\n",
" and_(aa.eacceptor1 == 'O2', aa.eacceptor2 == 'O2')))).all()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 79,
"text": [
"[AllAnalysis (fdr: 0.035516, fold change -0.233333): for Gene: yfbT/G7187 (b2293) Strain: delta-arcA-->wt on Condition: C:glucose, N:NH4Cl, e:anaerobic,\n",
" AllAnalysis (fdr: 0.000185, fold change -1.255000): for Gene: yfbV/G7189 (b2295) Strain: delta-arcA-->wt on Condition: C:glucose, N:NH4Cl, e:anaerobic,\n",
" AllAnalysis (fdr: 0.010148, fold change 0.716667): for Gene: yfbM/G7179 (b2272) Strain: wt-->delta-arcA on Condition: C:glucose, N:NH4Cl, e:NO3,\n",
" AllAnalysis (fdr: 0.023336, fold change 0.906667): for Gene: yfbS/G7186 (b2292) Strain: wt-->delta-arcA on Condition: C:glucose, N:NH4Cl, e:NO3,\n",
" AllAnalysis (fdr: 0.041744, fold change 0.236667): for Gene: yfbT/G7187 (b2293) Strain: wt-->delta-arcA on Condition: C:glucose, N:NH4Cl, e:NO3,\n",
" AllAnalysis (fdr: 0.023259, fold change -0.320000): for Gene: yfbU/G7188 (b2294) Strain: wt-->delta-arcA on Condition: C:glucose, N:NH4Cl, e:NO3]"
]
}
],
"prompt_number": 79
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"array([x.value for x in ome.query(ExpressionData).filter_by(bnum='b3327').all()]).mean()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 47,
"text": [
"2.2298529411764716"
]
}
],
"prompt_number": 47
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"unmapped = {\n",
" 'b4139':{'tu':'aspA', 'mistake':True, 'reason': 'dcuA is diff expressed in same operon'},\\\n",
" 'b0356':{'tu':'frmRAB', 'mistake':True, 'reason': 'have frmB under nitrate'},\\\n",
" 'b1223':{'tu':'narK', 'mistake':False, 'reason': 'have narX nearby but not narK or narG'},\\\n",
" 'b3042':{'tu':'yqiC', 'mistake':False, 'reason': 'have yqiAB but not on same operon'},\\\n",
" 'b4057':{'tu':'yjbQR', 'mistake':True, 'reason': 'have yjbQ, first gene in operon'},\\\n",
" 'b0189':{'tu':'yaeP-rof', 'mistake':False, 'reason': 'have yaeB on the other strand'},\\\n",
" 'b3865':{'tu':'yihA', 'mistake':False, 'reason': 'have csrC on the other strand'},\\\n",
" 'b1874':{'tu':'cutC', 'mistake':False, 'reason': 'have cutA on a different operon'},\\\n",
" 'b3023':{'tu':'ygiV', 'mistake':True, 'reason': 'have ygiW which is first gene in operon'},\\\n",
" 'b1273':{'tu':'yciN', 'mistake':False, 'reason': 'have yci genes on different operons'},\\\n",
" 'b1224':{'tu':'narGHJI', 'mistake':True, 'reason': 'have narHJI in the same operon'},\\\n",
" 'b1143':{'tu':'ymfI', 'mistake':False, 'reason': 'have ymfK nearby but different strand'},\\\n",
" 'b2290':{'tu':'yfbQ', 'mistake':False, 'reason': 'have yfb genes on different operons'}}\n"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 82
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"len(unmapped.keys())"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 87,
"text": [
"13"
]
}
],
"prompt_number": 87
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"aa = AllTUAnalysis\n",
"i = 0\n",
"for bnum in s12.index:\n",
" if not ome.query(aa).filter(and_(or_(aa.target1 == 'delta-arcA', aa.target2 == 'delta-arcA'),\\\n",
" or_(aa.target1 == 'wt', aa.target2 == 'wt'), aa.fdr < .05, aa.bnum == bnum,\\\n",
" or_(and_(aa.eacceptor1 == 'anaerobic', aa.eacceptor2 == 'anaerobic'),\\\n",
" and_(aa.eacceptor1 == 'NO3', aa.eacceptor2 == 'NO3'),\\\n",
" and_(aa.eacceptor1 == 'O2', aa.eacceptor2 == 'O2')))).all():\n",
" i+=1\n",
" exp_val = array([x.value for x in ome.query(ExpressionData).filter_by(bnum=bnum).all()]).mean()\n",
" print str(i)+'\\t'+bnum+'\\t'+str(s12['Operon'].ix[bnum])+'\\t'+str(exp_val)"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"1\tb4568\tytjA\tnan\n",
"2\tb4519\ticdC\tnan"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"3\tb3819\trarD\t2.25073529412"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"4\tb2172\tyeiQ\t2.67014705882"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"5\tb4490\tnan\tnan"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"6\tb0330\tprpR\t2.26308823529"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"7\tb1021\tpgaABCD\t2.69691176471"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"8\tb1534\tydeE\t2.47352941176"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"9\tb2152\tfolE-yeiB\t2.25042553191"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"10\tb4512\tybdD\tnan"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"11\tb3268\tyhdWXYZ\t3.29308823529"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"12\tb3324\tgspCDEFGHIJKLMO\t2.35029411765"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"13\tb1444\tydcW\t3.85955882353"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"14\tb4139\taspA\t10.0483823529"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"15\tb0527\tybcI\t2.25"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"16\tb0319\tyahDEFG\t2.24088235294"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"17\tb0443\tfadM\t2.76235294118"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"18\tb0356\tfrmRAB\t9.35617647059"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"19\tb2876\tyqeC\t2.29205882353"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"20\tb4280\tyjhBC\t3.69161764706"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"21\tb1223\tnarK\t6.62705882353"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"22\tb2419\tyfeKS\t2.25340425532"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"23\tb3042\tyqiC\t11.8351470588"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"24\tb4598\tyncL\tnan"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"25\tb4057\tyjbQR\t9.77426470588"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"26\tb0189\tyaeP-rof\t8.33529411765"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"27\tb3865\tyihA\t10.1757352941"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"28\tb1874\tcutC\t4.44808823529"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"29\tb3023\tygiV\t6.00823529412"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"30\tb4117\tadiA\t2.48558823529"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"31\tb4595\tyciY\tnan"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"32\tb4640\tupp-uraA\tnan"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"33\tb1273\tyciN\t5.92852941176"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"34\tb4606\typfM\tnan"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"35\tb1224\tnarGHJI\t9.61558823529"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"36\tb1143\tymfI\t7.29411764706"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"37\tb1634\ttppB\t2.29"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"38\tb4402\tyjjY\t3.79514705882"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"39\tb1974\tyodB\t3.06867647059"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"40\tb4641\tnan\tnan"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"41\tb4589\tylcI\tnan"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"42\tb2290\tyfbQ\t5.15426470588"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"43\tb4115\tadiC\t2.2685106383"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n"
]
}
],
"prompt_number": 50
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"s12"
],
"language": "python",
"metadata": {},
"outputs": [
{
"html": [
"<pre>\n",
"&lt;class 'pandas.core.frame.DataFrame'&gt;\n",
"Index: 229 entries, b0721 to b3491\n",
"Data columns (total 6 columns):\n",
"Strand 226 non-null values\n",
"Operon 227 non-null values\n",
"WT 229 non-null values\n",
"\u0394arcA 229 non-null values\n",
"Fold change 229 non-null values\n",
"P value 229 non-null values\n",
"dtypes: float64(4), object(2)\n",
"</pre>"
],
"metadata": {},
"output_type": "pyout",
"prompt_number": 56,
"text": [
"<class 'pandas.core.frame.DataFrame'>\n",
"Index: 229 entries, b0721 to b3491\n",
"Data columns (total 6 columns):\n",
"Strand 226 non-null values\n",
"Operon 227 non-null values\n",
"WT 229 non-null values\n",
"\u0394arcA 229 non-null values\n",
"Fold change 229 non-null values\n",
"P value 229 non-null values\n",
"dtypes: float64(4), object(2)"
]
}
],
"prompt_number": 56
},
{
"cell_type": "raw",
"metadata": {},
"source": [
"42/229 not diff expressed in our data\n",
"10/43 not measured\n",
"20/43 not measurably expressed\n",
"13/43 misses\n",
"5/13 FP\n",
"8 total misses"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [],
"language": "python",
"metadata": {},
"outputs": []
}
],
"metadata": {}
}
]
}
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