First I compiled a list of predicted CRP binding sites and associated them with genes predicted to be first in an operon (using data from DOOR and ProOpDB and confirmation by looking for similar expression of neighbouring genes in the RNA-seq data).
I pulled out genes that were very evidently CRP regulated (were differentially expressed, had CRP site). I decided on a cut-off using this list. I let all genes that were significant (padj < 0.1) in at least 2 out of 4 timepoints be considered truly significant. This reduced a lot of likely false positives (for example, a lot of genes were significant at the last timepoint which does not follow expected behaviour from CRP-regulated genes).
I uploaded the results to the Google Drive:
Scott/DE Results/CRP genes 1.xlsx
This file shows the raw differential expression analysis results on the first sheet. The second sheet shows the raw data of the genes that passed the cut-off I described above. The third sheet shows a prettier version with fold changes instead of log-fold changes (these are compared to KW20) and asterisks to represent significance. Genes are grouped by operons. The fourth sheet shows the predicted CRP binding sites and the last sheet is a simple list of genes that are directly (with a CRP site) and indirectly (could not find a strong CRP site) regulated by CRP. I'll also post some of the results here:
GENES WITH CRP-N SITES
| ID | Gene | CRP site 1 | CRP site 2 | CRP site 3 |
| HI0035 | AAATGTGACGAACGTATCATTT | |||
| HI0036 | AAATGTGACGAACGTATCATTT | |||
| HI0053 | TTTTGTGATATGGCTCACAAAA | |||
| HI0052 | ||||
| HI0051 | ||||
| HI0050m | ||||
| HI0049 | kdgK | |||
| HI0048 | ||||
| HI0047 | eda | |||
| HI0075 | nrdD | TAATTTGATATTTTTCTAATAA | TATTGATCACAAAATCAAAAAT | CATTGTGATATTGATCACAAAA |
| HI0082 | TTTCTTGATCCACGTCACATTA | |||
| HI0083 | ||||
| HI0131 | afuA | TATTATGAAATTCAACAAAATT | AACTGTGAACTTCATCACGGTA | |
| HI0129 | afuB | |||
| HI0126 | fbpC | |||
| HI0145 | AAATGAGAAGTTGATCACATTT | |||
| HI0144 | ||||
| HI0143 | ||||
| HI0142 | nanA | |||
| HI0146 | AAATGTGATCAACTTCTCATTT | |||
| HI0147 | ||||
| HI0289 | sdaC | AAATTTTAACTTGATCACAATT | ||
| HI0288 | sdaA | |||
| HI0398 | TTTTGTGACTCACTTCAAACTC | |||
| HI0399 | icc | |||
| HI0501 | rbsD | TTTTGTGATCAATATCCCAAAT | ||
| HI0502 | rbsA | |||
| HI0503 | rbsC | |||
| HI0504 | rbsB | |||
| HI0521 | AACTGTGATCTTCCTCACGTTT | |||
| HI0520 | ||||
| HI0534 | aspA | AAATGTGATCTTCATCAAGTTT | ||
| HI0591 | speF | TATTATGCCAAATTTAAAAATT | ||
| HI0590 | potE | |||
| HI0601 | tfoX | ATTTACGATCTGGCTCACAAAT | ||
| HI0604 | cyaA | ATTTACGATCTGGCTCACAAAT | ||
| HI0605 | gpsA | |||
| HI0606 | cysE | |||
| HI0607 | aroE | |||
| HI0608 | TTTGTTGCTCTCGATCACATTT | |||
| HI0685 | glpA | TATTGTGATCAATATCACAAAA | AAATGTGAAGTGTTTCACAAAT | |
| HI0684 | glpB | |||
| HI0683 | glpC | |||
| HI0740 | yhxB | AAATGTTAAGTAGATCAAAAAA | ||
| HI0745 | ansB | TTATGTGATCGAGATCATAAAT | ||
| HI0804 | TTTTGTTAAACACTTCACATTT | AATATTTATCTAGTTCAAAATT | ||
| HI0809 | pckA | AAATGAGATCTACTTAACATTT | ATTTTTGCTCTATATCACAATA | |
| HI0815 | uspA | AATTGTGATCTAGTACACAGTT | ||
| HI0822 | mglB | ATTTGTGACATGGATCACAAAT | ||
| HI0823 | mglA | |||
| HI0824 | mglC | |||
| HI0835 | frdA | TTTTTTGAGGTAGATCACAAAA | ||
| HI0834 | frdB | |||
| HI0833 | frdC | |||
| HI0832 | frdD | |||
| HI0884 | arcA | AACTATGATTTAGATCACAAAA | ||
| HI1010 | TTCTGTGATCTAGATCTCAGAT | |||
| HI1011 | ||||
| HI1012 | ||||
| HI1013 | ||||
| HI1014 | ||||
| HI1015 | gntP | |||
| HI1016 | ||||
| HI1111 | xylF | AAATAGGATCTAGATCACAAAA | ||
| HI1110 | xylG | |||
| HI1109 | xylH | |||
| HI1031 | AAATAGGATCTAGATCACAAAA | |||
| HI1030 | ||||
| HI1029 | ||||
| HI1028 | ||||
| HI1027 | lyx | |||
| HI1026 | ||||
| HI1025 | sgbE | |||
| HI1024 | ulaD | |||
| HI1089 | ccmA | AAATAGGATCTAGATCACAAAA | ||
| HI1090 | ccmB | |||
| HI1091 | ccmC | |||
| HI1092 | ccmD | |||
| HI1093 | ccmE | |||
| HI1094 | ccmF | |||
| HI1095 | dsbE | |||
| HI1096m | ccmH | |||
| HI1097m | ||||
| HI1126.1 | AAATGTGATACAAGTCACAAAT | |||
| HI1210 | mdh | AAATGTGAACTAGATCATAGAA | ||
| HI1218 | lctP | TTATGAGATATTGATCACATTT | ||
| HI1245 | AAGTTTGCAGTTCGTCACAATT | |||
| HI1350 | cdd | ATAAGTGATCAAGATCACAGTT | ||
| HI1356 | malQ | ATTATTGACGAAGATCACACTT | ||
| HI1357 | glgB | |||
| HI1358 | glgX | |||
| HI1359 | glgC | |||
| HI1360 | glgA | |||
| HI1398 | fumC | TTTTATGATCTATGTCACAAAA | ||
| HI1427 | TTTTGTGATCTCGATCACAAAT | |||
| HI1434.1 | cspD | AAAATTGATTTAGATCATTAAA | ||
| HI1645 | fbp | AAAATTGATTTAGATCATTAAA | ||
| HI1662 | sucA | AAAATTGATTTAGATCATTAAA | ||
| HI1661 | sucB |
OTHER GENES
| Competence genes | |
| HI0061 | rec2 |
| HI0299 | |
| HI0298 | |
| HI0297 | |
| HI0296 | hopD |
| HI0365 | |
| HI0366 | |
| HI0985 | dprA |
| HI1008 | |
| HI0439 | comA |
| HI0438 | comB |
| HI0437 | comC |
| HI0436 | comD |
| HI0435 | comE |
| HI0434 | comF |
| HI0660 | |
| HI0659 | |
| HI0658 | |
| HI0938 | |
| HI0939 | |
| HI0940 | |
| HI0941 | |
| HI0952 | radC |
| HI1117 | comM |
| HI1183 | |
| trp genes | |
| HI0287 | mtr |
| HI0830 | trpR |
| HI1387 | trpE |
| HI1388 | trpG |
| HI1388.1 | |
| HI1389 | trpD |
| HI1389.1 | trpC |
| HI1390 | hybG |
| HI1430 | |
| HI1431 | trpB |
| HI1432 | trpA |
| fuc genes | |
| HI0614 | fucI |
| HI0613 | fucK |
| HI0612 | fucU |
| Other | |
| HI0141 | nagB |
| HI0140 | nagA |
| HI0148 | |
| HI0300 | ampD |
| HI0410 | tyrR |
| HI0584 | |
| HI0623 | fmt |
| HI0738 | ilvD |
| HI0764 | ribB |
| HI0956 | |
| HI1056 | |
| HI1434 | ybaK |
| HI1456 | |
| HI1457 | |
| HI1492 | |
| HI1537 | licA |
| HI1538 | licB |
| HI1539 | licC |
| HI1540 | licD |
| HI1655 | |
| HI1664 | |
| HI1682 | sohB |
UPREGULATED:
HI0035, HI0047 (eda), HI0048, HI0049 (kdgK), HI0050m, HI0051, HI0052, HI0053, HI0061 (rec2),
HI0075 (nrdD), HI0082, HI0083, HI0126 (fbpC), HI0129 (afuB), HI0131 (afuA), HI0140 (nagA),
HI0141 (nagB), HI0142 (nanA), HI0143, HI0144, HI0145, HI0146, HI0147, HI0148, HI0288 (sdaA), HI0289 (sdaC), HI0296 (hopD), HI0297, HI0298, HI0299, HI0365, HI0366, HI0398, HI0399 (icc), HI0410 (tyrR), HI0434 (comF), HI0435 (comE), HI0436 (comD), HI0437 (comC), HI0438 (comB), HI0439 (comA), HI0501 (rbsD), HI0502 (rbsA), HI0503 (rbsC), HI0504 (rbsB), HI0520, HI0521, HI0534 (aspA), HI0590 (potE), HI0591 (speF), HI0601 (tfoX), HI0608, HI0612 (fucU), HI0613 (fucK), HI0614 (fucI), HI0623 (fmt), HI0658, HI0659, HI0660, HI0683 (glpC), HI0684 (glpB), HI0685 (glpA), HI0740 (yhxB), HI0745 (ansB), HI0804, HI0809 (pckA), HI0815 (uspA), HI0822 (mglB), HI0823 (mglA), HI0824 (mglC), HI0832 (frdD), HI0833 (frdC), HI0834 (frdB), HI0835 (frdA), HI0884 (arcA), HI0938, HI0939, HI0940, HI0941, HI0952 (radC), HI0985 (dprA), HI1008, HI1010, HI1011, HI1012, HI1013, HI1014, HI1015 (gntP), HI1016, HI1024 (ulaD), HI1025 (sgbE), HI1026, HI1027 (lyx), HI1028, HI1029, HI1030, HI1031, HI1110 (xylG), HI1111 (xylF), HI1117 (comM), HI1126.1, HI1183, HI1210 (mdh), HI1218 (lctP), HI1245, HI1350 (cdd), HI1356 (malQ), HI1357 (glgB), HI1358 (glgX), HI1359 (glgC), HI1360 (glgA), HI1398 (fumC), HI1427, HI1434.1 (cspD), HI1456, HI1457, HI1537 (licA), HI1538 (licB), HI1539 (licC), HI1540 (licD), HI1645 (fbp), HI1661 (sucB), HI1662 (sucA)
DOWNREGULATED:
HI0036, HI0300 (ampD), HI0584, HI0604 (cyaA), HI0605 (gpsA), HI0606 (cysE), HI0607 (aroE), HI0738 (ilvD), HI0956, HI1056, HI1089 (ccmA), HI1090 (ccmB), HI1091 (ccmC), HI1092 (ccmD), HI1093 (ccmE), HI1094 (ccmF), HI1095 (dsbE), HI1096m (ccmH), HI1097m, HI1434 (ybaK), HI1492, HI1655, HI1664, HI1682 (sohB)
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