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Table 1 Summarized list of most affected genes from induced TF RNA-Seq data with corresponding ChIP-Seq binding sites

From: Coordinated regulation of acid resistance in Escherichia coli

Gene symbol EcoCyc locus ChIP-Seq peak location Type Fold-change (FC) Log 2 (FC)
Nac-induced RNA-Seq
Top 20 over-expressed genes
  nac EG14265 2059466 genic 187.159 7.548
  yfgG EG14203 2627183 intergenic 138.340 7.112
  pyrL EG11279 4470803 intergenic 98.660 6.624
  ileY EG31121 2783527 intergenic 87.740 6.455
  shoB EG14494 2697790 genic 82.380 6.364
  ilvL EG11270 3948282 intergenic 67.590 6.079
  nrfF EG11949 4291501 genic 52.500 5.714
  ybgE EG12395 773855 intergenic 45.840 5.519
  yghG EG12991 3111175 genic 33.080 5.048
  ynaK EG14296 1423084 genic 25.970 4.699
  allR EG13616 532179 intergenic 17.160 4.101
  nanK EG12815 3368556 genic 16.050 4.005
  wcaE EG13573 2128058 genic 9.820 3.296
  rfbC EG11979 2108210 genic 8.854 3.146
  yqeJ EG13101 2987333 genic 7.346 2.877
  cmtA EG11792 3076545 genic 5.750 2.524
  hcaE EG13456 2666608 genic 5.032 2.331
  yqiC EG13031 3183243 intergenic 4.741 2.245
  yqeH EG13099 2985944 genic 4.544 2.184
  eutS EG14192 2574048 intergenic 3.761 1.911
Top 20 repressed genes
  yhfL EG12907 3497156 genic 0.008 −6.928
  chpS EG11250 4446394 intergenic 0.012 −6.349
  leuU EG30050 3320495 genic 0.013 −6.299
  fepE EG10297 617863 genic 0.013 −6.295
  bfd EG11181 3464917 genic 0.014 −6.137
  yhiJ EG12225 3631010 genic 0.017 −5.891
  yfhL EG13215 2697790 genic 0.019 −5.723
  scpB EG12972 3062091 genic 0.019 −5.718
  ampD EG10041 118719 intergenic 0.020 −5.644
  yafN EG13151 252250 genic 0.021 −5.555
  ybbC EG11769 526792 intergenic 0.027 −5.235
  yafO EG13152 252250 genic 0.029 −5.125
  ccmA EG12059 2295447 genic 0.030 −5.067
  yggP EG12976 3075011 genic 0.036 −4.779
  iraP EG11256 400152 intergenic 0.037 −4.750
  pabC EG11493 1152528 genic 0.038 −4.703
  rfbB EG12412 2110788 genic 0.039 −4.695
  macA EG13694 918441 intergenic 0.040 −4.658
  hfq EG10438 4398299 intergenic 0.044 −4.517
  yegR EG14061 2165875 intergenic 0.045 −4.477
CsiR-induced RNA-Seq
Top 20 over-expressed genes
  yehD EG11990 2190601 genic 55.750 55.750
  yjjP EG12592 4601377 intergenic 23.030 23.030
  ygiW EG13025 3167234 genic 5.438 5.438
  dinI EG12670 1120353 intergenic 4.335 4.335
  ychQ EG14293 1265792 genic 4.208676729 4.208676729
  bssS EG14335 1120353 intergenic 4.146456347 4.146456347
  gadX EG12243 3663762 genic 3.958 3.958
  yfbU EG14105 2410409 genic 3.063536927 3.063536927
  ppiB EG10758 553885 genic 2.985 2.985
  orn EG12480 4,389,621 intergenic 2.979 2.979
  gltF EG11514 3358941 intergenic 2.470 2.470
  murD EG10620 97136 genic 2.419 2.419
  pliG EG13892 1,226,238 intergenic 2.328431905 2.328431905
  hinT EG12172 1160988 intergenic 2.280 2.280
  ebgC EG10253 3223817 genic 2.159 2.159
  yfcV EG14125 2454000 intergenic 1.865631986 1.865631986
  rfbB EG12412 2110925 genic 1.850 1.850
  ydeO EG13797 1581558 genic 1.836799927 1.836799927
  smg EG11605 3430204 genic 1.748 1.748
  yfdV EG14144 2488614 genic 1.644414859 1.644414859
Top 20 repressed genes
  yobD EG13948 1903280 genic 0.164030959 −2.607959959
  yihM EG11839 4059288 genic 0.186 −2.423
  csiD EG13523 2786890 intergenic 0.245517248 −2.026103713
  ycjP EG13913 1372194 genic 0.269455258 −1.891882356
  yccU EG13723 1027171 genic 0.275398754 −1.860406061
  yjdP EG14407 4311501 genic 0.282972057 −1.8212685
  fhuE EG10306 1160988 intergenic 0.326 −1.617
  mrdA EG10606 667202 genic 0.371 −1.429
  yfcO EG14118 2447860 genic 0.381433124 −1.390497962
  baeS EG11617 2160863 genic 0.389 −1.360
  yfbP EG14100 2386855 genic 0.39350482 −1.345546788
  bdcR EG12529 4471822 genic 0.404 −1.306
  ycbU EG13713 1002250 genic 0.433672161 −1.205323262
  ydfI EG13821 1629426 genic 0.439353983 −1.186544321
  ttdR EG12694 3204662 genic 0.440 −1.185
  yfbT EG14104 2410409 genic 0.444846984 −1.168618925
  dinQ EG14431 3645540 genic 0.458480805 −1.12506676
  yciU EG14256 1304868 genic 0.463635491 −1.108937087
  gcvA EG11795 2940361 genic 0.484 −1.046
  oxc EG14143 2490338 genic 0.486938022 −1.038189938