{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "import matplotlib.pyplot as plt\n", "import pandas as pd\n", "import numpy as np\n", "import scipy.stats\n", "from matplotlib import rc\n", "import seaborn as sns\n", "rc('font',**{'family':'serif','serif':['Arial']})\n", "plt.rcParams['pdf.fonttype'] = 42" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "TS_rpkm=pd.read_csv('2019-12-11_RNAseq/TS_rpkm.csv',index_col=0)\n", "NTS_rpkm=pd.read_csv('2019-12-11_RNAseq/NTS_rpkm.csv',index_col=0)\n", "joined=TS_rpkm.join(NTS_rpkm)" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "L187R_NTS=NTS_rpkm[(NTS_rpkm['bm02_NTS']/NTS_rpkm['bm01_NTS']>2) & (NTS_rpkm['bm02_NTS']/NTS_rpkm['bm01_NTS']<=4) ]\n", "L187R_NTS2=NTS_rpkm[NTS_rpkm['bm02_NTS']/NTS_rpkm['bm01_NTS']>4]" ] }, { "cell_type": "code", "execution_count": 39, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | bm01_NTS | \n", "bm02_NTS | \n", "bm03_NTS | \n", "bm04_NTS | \n", "bm05_NTS | \n", "bm06_NTS | \n", "bm07_NTS | \n", "bm08_NTS | \n", "bm09_NTS | \n", "bm10_NTS | \n", "bm11_NTS | \n", "bm12_NTS | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|
Gene name | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
aaeB | \n", "0.151995 | \n", "0.440346 | \n", "1.629708 | \n", "1.603285 | \n", "0.803554 | \n", "0.440519 | \n", "3.492165 | \n", "1.035073 | \n", "2.167498 | \n", "1.658221 | \n", "1.649347 | \n", "0.792721 | \n", "
aat | \n", "0.212340 | \n", "0.442923 | \n", "0.403471 | \n", "0.407239 | \n", "0.164280 | \n", "0.289606 | \n", "1.910506 | \n", "0.304424 | \n", "0.946260 | \n", "0.706748 | \n", "1.112356 | \n", "0.325719 | \n", "
abgA | \n", "0.038038 | \n", "0.105791 | \n", "0.185852 | \n", "0.175082 | \n", "0.147141 | \n", "0.077818 | \n", "1.980093 | \n", "0.190865 | \n", "0.237311 | \n", "0.211005 | \n", "0.341591 | \n", "0.245060 | \n", "
abgB | \n", "0.137935 | \n", "0.455559 | \n", "0.870524 | \n", "0.396812 | \n", "0.747008 | \n", "0.634928 | \n", "2.426711 | \n", "0.469663 | \n", "0.676156 | \n", "0.994719 | \n", "1.316132 | \n", "1.015612 | \n", "
abgR | \n", "1.152436 | \n", "3.624904 | \n", "5.407376 | \n", "1.768172 | \n", "0.382113 | \n", "0.392945 | \n", "5.977997 | \n", "3.068379 | \n", "4.450895 | \n", "2.009199 | \n", "0.862443 | \n", "0.707111 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
ytiA | \n", "0.775551 | \n", "2.022166 | \n", "2.052567 | \n", "1.784881 | \n", "0.750019 | \n", "1.983292 | \n", "4.485814 | \n", "0.972893 | \n", "1.555254 | \n", "2.366216 | \n", "1.523538 | \n", "3.390518 | \n", "
ytjA | \n", "0.309498 | \n", "0.860781 | \n", "1.512211 | \n", "1.068434 | \n", "0.239447 | \n", "0.316588 | \n", "2.088504 | \n", "0.443715 | \n", "0.275846 | \n", "0.343375 | \n", "1.389705 | \n", "1.139409 | \n", "
ytjC | \n", "0.693141 | \n", "2.623920 | \n", "6.397097 | \n", "7.532984 | \n", "1.370436 | \n", "1.654378 | \n", "54.791754 | \n", "5.962382 | \n", "10.914018 | \n", "7.006552 | \n", "12.362893 | \n", "6.946521 | \n", "
zipA | \n", "0.151610 | \n", "0.351384 | \n", "0.164615 | \n", "0.174460 | \n", "0.234590 | \n", "0.155083 | \n", "0.146153 | \n", "0.398489 | \n", "0.360334 | \n", "0.336410 | \n", "0.170189 | \n", "0.232562 | \n", "
zwf | \n", "0.135130 | \n", "0.469782 | \n", "0.660247 | \n", "0.349867 | \n", "0.209090 | \n", "0.103669 | \n", "1.074695 | \n", "0.556976 | \n", "0.662403 | \n", "0.487244 | \n", "0.492992 | \n", "0.621847 | \n", "
1364 rows × 12 columns
\n", "\n", " | bm01_NTS | \n", "bm02_NTS | \n", "bm03_NTS | \n", "bm04_NTS | \n", "bm05_NTS | \n", "bm06_NTS | \n", "bm07_NTS | \n", "bm08_NTS | \n", "bm09_NTS | \n", "bm10_NTS | \n", "bm11_NTS | \n", "bm12_NTS | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|
Gene name | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
aaeX | \n", "3.681955 | \n", "4.949493 | \n", "9.394829 | \n", "7.908869 | \n", "13.863157 | \n", "15.316286 | \n", "11.358169 | \n", "3.695077 | \n", "8.969736 | \n", "12.527273 | \n", "18.737051 | \n", "11.973617 | \n", "
abgB | \n", "0.137935 | \n", "0.455559 | \n", "0.870524 | \n", "0.396812 | \n", "0.747008 | \n", "0.634928 | \n", "2.426711 | \n", "0.469663 | \n", "0.676156 | \n", "0.994719 | \n", "1.316132 | \n", "1.015612 | \n", "
abpB | \n", "0.204871 | \n", "1.820165 | \n", "5.079160 | \n", "3.981532 | \n", "1.215175 | \n", "1.071104 | \n", "27.912869 | \n", "6.771777 | \n", "9.251473 | \n", "2.904336 | \n", "3.986274 | \n", "2.786451 | \n", "
actP | \n", "0.030218 | \n", "0.189095 | \n", "0.590579 | \n", "0.347722 | \n", "0.561081 | \n", "0.401830 | \n", "2.738233 | \n", "0.584849 | \n", "0.996490 | \n", "0.804610 | \n", "0.644498 | \n", "0.750911 | \n", "
ada | \n", "0.046832 | \n", "0.097687 | \n", "0.343232 | \n", "0.269452 | \n", "0.217393 | \n", "0.239523 | \n", "0.993217 | \n", "0.234994 | \n", "0.125219 | \n", "0.259790 | \n", "0.630853 | \n", "0.387924 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
ytfI | \n", "0.159368 | \n", "2.068445 | \n", "7.137863 | \n", "2.017267 | \n", "0.575388 | \n", "1.249812 | \n", "36.410772 | \n", "4.264965 | \n", "14.488066 | \n", "2.770064 | \n", "3.995400 | \n", "2.737983 | \n", "
ytfQ | \n", "0.052123 | \n", "0.217446 | \n", "0.933796 | \n", "0.299892 | \n", "0.241952 | \n", "0.373216 | \n", "2.411829 | \n", "0.261541 | \n", "0.418096 | \n", "0.289139 | \n", "0.585100 | \n", "0.335804 | \n", "
zinT | \n", "0.153320 | \n", "1.492463 | \n", "13.484271 | \n", "9.791788 | \n", "0.652401 | \n", "0.627330 | \n", "198.497835 | \n", "11.924678 | \n", "48.988893 | \n", "2.041233 | \n", "13.338491 | \n", "3.316119 | \n", "
zraR | \n", "0.075214 | \n", "0.313779 | \n", "0.704367 | \n", "0.432749 | \n", "0.261856 | \n", "0.346215 | \n", "1.848917 | \n", "0.512198 | \n", "0.837946 | \n", "0.542403 | \n", "0.379940 | \n", "0.311510 | \n", "
zupT | \n", "0.322310 | \n", "1.434265 | \n", "4.619450 | \n", "4.747368 | \n", "1.845260 | \n", "3.099118 | \n", "63.198182 | \n", "3.511837 | \n", "9.881907 | \n", "2.002504 | \n", "14.182896 | \n", "8.068726 | \n", "
540 rows × 12 columns
\n", "\n", " | bm01_NTS | \n", "bm02_NTS | \n", "bm03_NTS | \n", "bm04_NTS | \n", "bm05_NTS | \n", "bm06_NTS | \n", "bm07_NTS | \n", "bm08_NTS | \n", "bm09_NTS | \n", "bm10_NTS | \n", "bm11_NTS | \n", "bm12_NTS | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|
Gene name | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
aaeB | \n", "0.151995 | \n", "0.440346 | \n", "1.629708 | \n", "1.603285 | \n", "0.803554 | \n", "0.440519 | \n", "3.492165 | \n", "1.035073 | \n", "2.167498 | \n", "1.658221 | \n", "1.649347 | \n", "0.792721 | \n", "
aat | \n", "0.212340 | \n", "0.442923 | \n", "0.403471 | \n", "0.407239 | \n", "0.164280 | \n", "0.289606 | \n", "1.910506 | \n", "0.304424 | \n", "0.946260 | \n", "0.706748 | \n", "1.112356 | \n", "0.325719 | \n", "
abgA | \n", "0.038038 | \n", "0.105791 | \n", "0.185852 | \n", "0.175082 | \n", "0.147141 | \n", "0.077818 | \n", "1.980093 | \n", "0.190865 | \n", "0.237311 | \n", "0.211005 | \n", "0.341591 | \n", "0.245060 | \n", "
abgB | \n", "0.137935 | \n", "0.455559 | \n", "0.870524 | \n", "0.396812 | \n", "0.747008 | \n", "0.634928 | \n", "2.426711 | \n", "0.469663 | \n", "0.676156 | \n", "0.994719 | \n", "1.316132 | \n", "1.015612 | \n", "
abgR | \n", "1.152436 | \n", "3.624904 | \n", "5.407376 | \n", "1.768172 | \n", "0.382113 | \n", "0.392945 | \n", "5.977997 | \n", "3.068379 | \n", "4.450895 | \n", "2.009199 | \n", "0.862443 | \n", "0.707111 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
znuB | \n", "0.444336 | \n", "1.853696 | \n", "3.773465 | \n", "2.045223 | \n", "1.276847 | \n", "0.844099 | \n", "17.562056 | \n", "2.775623 | \n", "7.071836 | \n", "4.366332 | \n", "2.778966 | \n", "2.453721 | \n", "
zraR | \n", "0.075214 | \n", "0.313779 | \n", "0.704367 | \n", "0.432749 | \n", "0.261856 | \n", "0.346215 | \n", "1.848917 | \n", "0.512198 | \n", "0.837946 | \n", "0.542403 | \n", "0.379940 | \n", "0.311510 | \n", "
zupT | \n", "0.322310 | \n", "1.434265 | \n", "4.619450 | \n", "4.747368 | \n", "1.845260 | \n", "3.099118 | \n", "63.198182 | \n", "3.511837 | \n", "9.881907 | \n", "2.002504 | \n", "14.182896 | \n", "8.068726 | \n", "
zur | \n", "0.870800 | \n", "8.005685 | \n", "8.036742 | \n", "4.230861 | \n", "0.973131 | \n", "0.791776 | \n", "46.636495 | \n", "15.119922 | \n", "16.298454 | \n", "5.582013 | \n", "5.756480 | \n", "2.315323 | \n", "
zwf | \n", "0.135130 | \n", "0.469782 | \n", "0.660247 | \n", "0.349867 | \n", "0.209090 | \n", "0.103669 | \n", "1.074695 | \n", "0.556976 | \n", "0.662403 | \n", "0.487244 | \n", "0.492992 | \n", "0.621847 | \n", "
2213 rows × 12 columns
\n", "\n", " | bm01_NTS | \n", "bm02_NTS | \n", "bm03_NTS | \n", "bm04_NTS | \n", "bm05_NTS | \n", "bm06_NTS | \n", "bm07_NTS | \n", "bm08_NTS | \n", "bm09_NTS | \n", "bm10_NTS | \n", "bm11_NTS | \n", "bm12_NTS | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|
Gene name | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
aaeB | \n", "0.151995 | \n", "0.440346 | \n", "1.629708 | \n", "1.603285 | \n", "0.803554 | \n", "0.440519 | \n", "3.492165 | \n", "1.035073 | \n", "2.167498 | \n", "1.658221 | \n", "1.649347 | \n", "0.792721 | \n", "
aat | \n", "0.212340 | \n", "0.442923 | \n", "0.403471 | \n", "0.407239 | \n", "0.164280 | \n", "0.289606 | \n", "1.910506 | \n", "0.304424 | \n", "0.946260 | \n", "0.706748 | \n", "1.112356 | \n", "0.325719 | \n", "
abgA | \n", "0.038038 | \n", "0.105791 | \n", "0.185852 | \n", "0.175082 | \n", "0.147141 | \n", "0.077818 | \n", "1.980093 | \n", "0.190865 | \n", "0.237311 | \n", "0.211005 | \n", "0.341591 | \n", "0.245060 | \n", "
abgB | \n", "0.137935 | \n", "0.455559 | \n", "0.870524 | \n", "0.396812 | \n", "0.747008 | \n", "0.634928 | \n", "2.426711 | \n", "0.469663 | \n", "0.676156 | \n", "0.994719 | \n", "1.316132 | \n", "1.015612 | \n", "
abgR | \n", "1.152436 | \n", "3.624904 | \n", "5.407376 | \n", "1.768172 | \n", "0.382113 | \n", "0.392945 | \n", "5.977997 | \n", "3.068379 | \n", "4.450895 | \n", "2.009199 | \n", "0.862443 | \n", "0.707111 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
znuB | \n", "0.444336 | \n", "1.853696 | \n", "3.773465 | \n", "2.045223 | \n", "1.276847 | \n", "0.844099 | \n", "17.562056 | \n", "2.775623 | \n", "7.071836 | \n", "4.366332 | \n", "2.778966 | \n", "2.453721 | \n", "
zraR | \n", "0.075214 | \n", "0.313779 | \n", "0.704367 | \n", "0.432749 | \n", "0.261856 | \n", "0.346215 | \n", "1.848917 | \n", "0.512198 | \n", "0.837946 | \n", "0.542403 | \n", "0.379940 | \n", "0.311510 | \n", "
zupT | \n", "0.322310 | \n", "1.434265 | \n", "4.619450 | \n", "4.747368 | \n", "1.845260 | \n", "3.099118 | \n", "63.198182 | \n", "3.511837 | \n", "9.881907 | \n", "2.002504 | \n", "14.182896 | \n", "8.068726 | \n", "
zur | \n", "0.870800 | \n", "8.005685 | \n", "8.036742 | \n", "4.230861 | \n", "0.973131 | \n", "0.791776 | \n", "46.636495 | \n", "15.119922 | \n", "16.298454 | \n", "5.582013 | \n", "5.756480 | \n", "2.315323 | \n", "
zwf | \n", "0.135130 | \n", "0.469782 | \n", "0.660247 | \n", "0.349867 | \n", "0.209090 | \n", "0.103669 | \n", "1.074695 | \n", "0.556976 | \n", "0.662403 | \n", "0.487244 | \n", "0.492992 | \n", "0.621847 | \n", "
2213 rows × 12 columns
\n", "\n", " | bm01_NTS | \n", "bm02_NTS | \n", "bm03_NTS | \n", "bm04_NTS | \n", "bm05_NTS | \n", "bm06_NTS | \n", "bm07_NTS | \n", "bm08_NTS | \n", "bm09_NTS | \n", "bm10_NTS | \n", "bm11_NTS | \n", "bm12_NTS | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|
Gene name | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
aaeA | \n", "0.801971 | \n", "0.929358 | \n", "1.480301 | \n", "1.230457 | \n", "2.812732 | \n", "1.640684 | \n", "2.989339 | \n", "0.613203 | \n", "1.572497 | \n", "1.423607 | \n", "2.400670 | \n", "1.968292 | \n", "
aaeB | \n", "0.151995 | \n", "0.440346 | \n", "1.629708 | \n", "1.603285 | \n", "0.803554 | \n", "0.440519 | \n", "3.492165 | \n", "1.035073 | \n", "2.167498 | \n", "1.658221 | \n", "1.649347 | \n", "0.792721 | \n", "
aaeR | \n", "2.467320 | \n", "2.834371 | \n", "11.138111 | \n", "12.838078 | \n", "7.718494 | \n", "4.937948 | \n", "65.202237 | \n", "4.344732 | \n", "19.408955 | \n", "16.721890 | \n", "20.893063 | \n", "12.094723 | \n", "
aaeX | \n", "3.681955 | \n", "4.949493 | \n", "9.394829 | \n", "7.908869 | \n", "13.863157 | \n", "15.316286 | \n", "11.358169 | \n", "3.695077 | \n", "8.969736 | \n", "12.527273 | \n", "18.737051 | \n", "11.973617 | \n", "
aas | \n", "0.207718 | \n", "0.320949 | \n", "0.808170 | \n", "0.929539 | \n", "0.892797 | \n", "0.779078 | \n", "3.537591 | \n", "0.397063 | \n", "0.822809 | \n", "0.870605 | \n", "1.139957 | \n", "1.125820 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
zraR | \n", "0.075214 | \n", "0.313779 | \n", "0.704367 | \n", "0.432749 | \n", "0.261856 | \n", "0.346215 | \n", "1.848917 | \n", "0.512198 | \n", "0.837946 | \n", "0.542403 | \n", "0.379940 | \n", "0.311510 | \n", "
zraS | \n", "0.107006 | \n", "0.198405 | \n", "0.755204 | \n", "0.246268 | \n", "0.331146 | \n", "0.291886 | \n", "1.581702 | \n", "0.153411 | \n", "0.540436 | \n", "0.751886 | \n", "0.600597 | \n", "0.295455 | \n", "
zupT | \n", "0.322310 | \n", "1.434265 | \n", "4.619450 | \n", "4.747368 | \n", "1.845260 | \n", "3.099118 | \n", "63.198182 | \n", "3.511837 | \n", "9.881907 | \n", "2.002504 | \n", "14.182896 | \n", "8.068726 | \n", "
zur | \n", "0.870800 | \n", "8.005685 | \n", "8.036742 | \n", "4.230861 | \n", "0.973131 | \n", "0.791776 | \n", "46.636495 | \n", "15.119922 | \n", "16.298454 | \n", "5.582013 | \n", "5.756480 | \n", "2.315323 | \n", "
zwf | \n", "0.135130 | \n", "0.469782 | \n", "0.660247 | \n", "0.349867 | \n", "0.209090 | \n", "0.103669 | \n", "1.074695 | \n", "0.556976 | \n", "0.662403 | \n", "0.487244 | \n", "0.492992 | \n", "0.621847 | \n", "
4419 rows × 12 columns
\n", "