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 |