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Table 2 Functional investigation of modules identified.

From: Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach

index Operons included Biological function description
1 aceBAK, acs, adhE, fruBKA, fruR, icdA, iclMR, mlc, ppsA, ptsG, ptsHI_crr, pykF Hexose PTS transport system, PEP generation, Acetate usage, glyoxylate shunt
2 acnA, fpr, fumC, marRAB, nfo, sodA, soxR, soxS, zwf Oxidative stress response
3 ada_alkB, aidB, alkA, ahpCF, dps, gorA, katG, oxyR Oxidative stress response, Alkylation
4 alaWX, aldB, argU, argW, argX_hisR_leuT_proM, aspV, dnaA, leuQPV, leuX, lysT_valT_lysW, metT_leuW_glnUW_metU_glnVX, metY_yhbC_nusA_infB, nrdAB, pdhR_aceEF_lpdA, pheU, pheV, proK, proL, proP, sdhCDAB_b0725_sucABCD, serT, serX, thrU_tyrU_glyT_thrT, thrW, tyrTV, valUXY_lysV, yhdG_fis rRNA, tRNA genes, DNA synthesis system, pyruvate dehydrogenase and ketoglutarate dehydrogenase system
5 araBAD, araC, araE, araFGH, araJ Arabinose uptake and usage
6 argCBH, argD, argE, argF, argI, argR, carAB Arginine usage, urea cycle
7 caiF, caiTABCDE, fixABCX Carnitine usage
8 clpP, dnaKJ, grpE, hflB, htpG, htpY, ibpAB, lon, mopA, mopB, rpoH Heat shock response
9 codBA, cvpA_purF_ubiX, glnB, glyA, guaBA, metA, metH, metR, prsA, purC, purEK, purHD, purL, purMN, purR, pyrC, pyrD, speA, ycfC_purB, metC, metF, metJ Purine synthesis, purine and pyrimidine salvage pathway, methionine synthesis
10 cpxAR, cpxP, dsbA, ecfI, htrA, motABcheAW, ppiA, skp_lpxDA_fabZ, tsr, xprB_dsbC_recJ Stress response, Conjugative plasmid expression, cell motility and Chemotaxis
11 dctA, dcuB_fumB, frdABCD, yjdHG C4 dicarboxylate uptake
12 edd_eda, gntKU, gntR, gntT Gluconate usage, ED pathway
13 csgBA, csgDEFG, envY_ompT, evgA, gcvA, gcvR, gcvTHP, gltBDF, ilvIH, kbl_tdh, livJ, livKHMGF, lrp, lysU, ompC, ompF, oppABCDF, osmC, sdaA, serA, stpA Amino acid uptake and usage
14 fdhF, fhlA, hycABCDEFGH, hypABCDE Formate hydrogenlyase system
15 flgAMN, flgBCDEFGHIJ, flgKL, flgMN, flhBAE, flhDC, fliAZY, fliC, fliDST, fliE, fliFGHIJK, fliLMNOPQR, tarTapcheRBYZ Flagella motility system
16 ftsQAZ, rcsAB, wza_wzb_b2060_wcaA_wcaB Capsule synthesis, cell division
17 gdhA, glnALG, glnHPQ, nac, putAP Glutamine and proline utilization
18 glmUS, manXYZ, nagBACD, nagE Glucosamine, mannose utilization
19 glpACB, glpD, glpFK, glpR, glpTQ Glycerol phosphate utilization
20 lysA, lysR, tdcABCDEFG, tdcR Serine, threonine usage
21 malEFG, malK_lamB_malM, malPQ, malS, malT, malZ Maltose utilization
22 rhaBAD, rhaSR, rhaT Rhamnose utilization
23 appCBA, appY, betIBA, betT, cydAB, cyoABCDE, fadBA, focA_pflB, fumA, glcC, glcDEFGB, gltA, lctPRD, mdh, nuoABCEFGHIJKLMN, fabA, fadL, fadR, uspA Oxidative phosphorylation, Glycolate, lactose utilization, fatty acid degradation
24 cytR, deoCABD, deoR, nupC, nupG, tsx, udp Nucleosides uptake and usage
25 cirA, entCEBA, fecABCDE, fecIR, fepA_entD, fepB, fepDGC, fhuACDB, fur, tonB Iron uptake system
26 galETKM, galR, galS, mglBAC Galactose uptake and usage
27 dmsABC, fdnGHI, narGHJI, narK, nirBDC_cysG, nrfABCDEFG, torCAD, torR Nitrogen metabolism, Nitrate and nitrite reductase,
28 narZYWV, nhaA, nhaR, osmY intracellular pH regulation
29 aslB, inaA, mdlA, rob, ybaO, ybiS, yfhD Stress response
30 cutC, dapA_nlpB_purA, ecfABC, ecfD, ecfF, ecfG, ecfH, ecfJ, ecfK, ecfLM, fkpA, ksgA_epaG_epaH, lpxDA_fabZ, mdoGH, nlpB_purA, ostA_surA_pdxA, rfaDFCL, rfbO, rpoE_rseABC, uppS_cdsA_ecfE RpoE regulated stress response, lipopolysaccharide synthesis
31 ansB, cpdB, cyaA, dadAX, epd_pgk, glgCAP, glgS, ivbL_ilvBN, ompA, speC, srlAEBD_gutM_srlR_gutQ, tnaLAB, ubiG, yhfA Sorbitol and Glycogen metabolism
32 atoC, atoB, hydHG, hypA, pspABCDE, pspF, rtcAB, rtcR, zraP Phage shock protein, Zn-resistence system, Acetoacetate metabolism
33 dsdC, dsdXA, ebgAC, ebgR, fucAO, fucPIKUR, lacI, lacZYA, malI, malXY, melAB, melR, uhpA, uhpT, yiaJ, yiaKLMNOPQRS Lactose, maltose, fucose, dehydroascorbate, xylulose, melibiose transport and metabolism
34 aroF_tyrA, aroG, aroH, aroL_yaiA_aroM, aroP, mtr, trpLEDCBA, trpR, tyrP, tyrR Aromatic amino acid synthesis
35 bioA, bioBFCD, birA_murA Biotin synthesis
36 cbl, cysB, cysDNC, cysJIH, cysK, cysPUWAM, ssuEADCB, tauABCD Sulfur metabolism, cysteine synthesis, Taurine utilization
37 exuR, exuT, uidR, uidABC, uxaCA, uxuABR Utilization of hexUronide
38 lexA_dinF, polB, recA, recN, rpsU_dnaG_rpoD, ssb, sulA, umuDC, uvrA, uvrB, uvrC, uvrD DNA recombination and repair, UV resistent
39 phnCDE_f73_phnFGHIJKLMNOP, phoA, phoBR, phoE, pstSCAB_phoU Phosphate metabolism