Table 1.
Gene Ontology Pathway Enrichment Analysis of OxyR Regulon Genes
| Pathway | False discovery rate | Genes |
|---|---|---|
| Oxidation–reduction process | 2.02E-09 | aceA, aceB, aceE, acnA, acnB, cyoB, cyoC, cyoD, cysD, cysI, dadA, fdnG, fdnH, fdnI, fdoG, fdoI, fumA, gcd, gcvP, glpD, gltA, hcp, hcr, katG, leuB, lipA, lpdA, maeB, msrB, napB, narI, nrdD, sdhB, ssuE, sthA, sucD, tpx, ybiC |
| Generation of precursor metabolites and energy | 2.12E-09 | aceA, aceB, aceE, acnA, acnB, cyoB, cyoC, cyoD, fdnG, fdnH, fdnI, fdoG, fdoI, fumA, gltA, gpmA, lpdA, napB, narI, sdhB, sucD |
| Cellular respiration | 2.12E-09 | aceA, aceB, acnA, acnB, cyoB, cyoC, cyoD, fdnG, fdnH, fdnI, fdoG, fdoI, fumA, gltA, nap, narI, sdhB, sucD |
| Aerobic respiration | 2.01E-06 | aceA, aceB, acnA, acnB, cyoB, cyoC, cyoD, fumA, gltA, sdhB, sucD |
| Tricarboxylic acid cycle | 1.51E-05 | aceA, aceB, acnA, acnB, fumA, gltA, sdhB, sucD |
| Branched-chain amino acid biosynthetic process | 0.000131 | ilvA, ilvD, ilvE, ilvM, ilvN, leuB, leuD |
| Single-organism metabolic process | 0.000247 | aceA, aceB, aceE, acnA, acnB, allE, cyoB, cyoC, cyoD, cyoE, cysD, cysI, dadA, dadB, fdnG, fdnH, fdnI, fdoG, fdoI, fumA, gcd, gcvP, glpD, glpE, gltA, gntT, gpmA, hchA, hcp, hcr, ilvA, ilvD, ilvE, ilvM, ilvN, katG, leuB, leuD, lipA, lpdA, maeB, metH, msrB, napB, narI, nrdD, sdhB, speD, ssuE, sthA, sucD, thiH, tpx, ybiC, ynhG |
| Oxoacid metabolic process | 0.000523 | aceA, aceB, aceE, acnA, acnB, cysI, dadA, dadB, fumA, gcvP, gltA, gntT, gpmA, hchA, ilvA, ilvD, ilvE, ilvM, ilvN, leuB, leuD, lipA, lpdA, maeB, metH, narI, sdhB, sucD |
| Carboxylic acid metabolic process | 0.000592 | aceA, aceB, aceE, acnA, acnB, cysI, dadA, dadB, fumA, gcvP, gltA, gntT, gpmA, hchA, ilvA, ilvD, ilvE, ilvM, ilvN, leuB, leuD, lipA, lpdA, maeB, metH, sdhB, sucD |
| Isoleucine biosynthetic process | 0.00063 | ilvA, ilvD, ilvE, ilvM, ilvN |
| Anaerobic respiration | 0.00102 | acnA, fdnG, fdnH, fdnI, fdoG, fdoI, napB, narI |
| Glyoxylate cycle | 0.00244 | aceA, aceB, acnA, acnB |
| Small-molecule metabolic process | 0.00453 | aceA, aceB, aceE, acnA, acnB, allE, cysI, dadA, dadB, fumA, gcvP, glpD, glpE, gltA, gntT, gpmA, hchA, ilvA, ilvD, ilvE, ilvM, ilvN, leuB, leuD, lipA, lpdA, maeB, metH, narI, nrdD, sdhB, speD, sthA, sucD, thiH |
| Valine biosynthesis | 0.00635 | ilvD, ilvE, ilvM, ilvN |
| Cellular response to starvation | 0.0284 | leuB, psiE, ssuE, tauA, tauB |
| Response to oxidative stress | 0.0361 | acnA, clpA, cysD, hcp, katG, lpdA, msrB, tpx |
| Electron transport coupled proton transport | 0.0405 | cyoB, cyoC, cyoD |
| Respiratory electron transport chain | 0.0419 | cyoB, cyoC, cyoD, fdnI, fdoI |
| Alpha-amino acid metabolic process | 0.0419 | cysI, dadA, dadB, gcvP, ilvA, ilvD, ilvE, ilvM, ilvN, leuB, leuD, lpdA, metH |
| Taurine transport | 0.0485 | tauA, tauB |
| Leucine biosynthesis | 0.0498 | ilvE, leuB, leuD |
The OxyR-dependent genes induced under anaerobic growth on nitrate were grouped by biological processes by using STRING.