Environment and Gene Regulatory Influence Network (EGRIN) model for C. difficile 630

The Environment and Gene Regulatory Influence Network (EGRIN) model of C. difficile 630 was inferred using cMonkey2 and a compendium of 136 transcriptomes (retrieved from the Gene Expression Omnibus repository) with 4,070 sequence features including 35 rRNAs and 90 tRNAs . The C. difficile EGRIN model groups genes in subsets (406 modules in total), that are co-regulated in specific environments, and also identifies the associated, putative cis-acting gene regulatory elements (GREs), which represent potential TF binding locations. Transcriptome compendium included conditions: response to iron limitation, response to oxygen, in vivo vs in vitro growth, short term infection (0, 30, 60, 120 mins), response to commensals and host diet, transition from exponential to stationary phase, fur KO, codY KO, sporulation TF (and sigma factors) KOs.

Explore Regulatory Modules

Displaying 41 - 50 of 406

Candidate transcriptional regulators for each module were determined with a linear regression based approach (Inferelator) and by evaluating the statistical significance of the overlap (Hypergeometric) between modules and putative TF and alternative sigma factor regulons (CcpA, CodY, Fur, PrdR, SigB, SigD, SigE, SigF, SigG, SigH, SigK, Spo0A) compiled from available literature.

* Given that translation start was used to define the 3' end of putative promoters, some cis-regulatory motifs are likely to be ribosome binding sites (i.e., Shine-Dalgarno sequence). RBS is typically a six nucleotide sequence 5'-GGAGGA-3'.

Title	Gene Count	Motif 1 e-value	Motif 2 e-value	Residual	TF Influences
Module_62	9 CD630_06012 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_20060 - Type: Gene Product:Fragment of putative topoisomerase (C-terminalregion) \| Pathway: \| COG: Function unknown CD630_19901 - Type: Gene Product:Fragment of transcriptional regulator,beta-lactams repressor (Part 2) \| Pathway: \| COG: Transcription CD630_23052 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_20131 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_14220 - Type: Gene Product:Transcriptional regulator, MerR family \| Pathway: \| COG: Transcription CD630_20090 - Type: Gene Product:Fragment of putative topoisomerase (C-terminalregion) \| Pathway: \| COG: Replication, recombination and repair CD630_11230 - Type: Gene Product:Putative phosphoesterase \| Pathway: \| COG: Function unknown CD630_06620 - Type: Gene Product:Fragment of phage endolysin CwlH \| Pathway: \| COG:	`NA`	`NA`	0.46	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_14220 - Type: Gene Product:Transcriptional regulator, MerR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_334	6 CD630_06740 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_09780 - Type: Gene Product:Transcriptional regulator, beta-lactams repressorPhage-type \| Pathway: \| COG: CD630_18441 - Type: Gene Product:Fragment of putative methyltransferase(N-terminal region) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_17591 - Type: Gene Product:Fragment of conserved hypothetical protein,UPF0027 family (C-terminal region) \| Pathway: \| COG: CD630_01960 - Type: Gene Product:Fragment of conserved hypothetical protein,DUF111 family (Part 1) \| Pathway: \| COG: Function unknown, Function unknown	`NA`	`NA`	0.63	Inferelator: 0 Hypergeometric: 0 TF Influences from Inferelator `No TF influences from Inferelator` TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_158	13 CD630_19110 - eutW Type: Gene Product:Two-component sensor histidine kinase,Ethanolamine specific \| Pathway: \| COG: Signal transduction mechanisms CD630_19160 - eutK Type: Gene Product:Ethanolamine carboxysome structural protein, BMCfamily \| Pathway: \| COG: Amino acid transport and metabolism CD630_19130 - eutB Type: Gene Product:Ethanolamine ammonia lyase large subunit \| Pathway: \| COG: Amino acid transport and metabolism CD630_19120 - eutA Type: Gene Product:Ethanolamine reactivating factor for ammonialyase eutBC \| Pathway: \| COG: Amino acid transport and metabolism CD630_19080 - eutS Type: Gene Product:Ethanolamine carboxysome structural protein, BMCfamily \| Pathway: \| COG: Amino acid transport and metabolism CD630_19100 - eutV Type: Gene Product:Two-component response regulator, Ethanolaminespecific \| Pathway: \| COG: Signal transduction mechanisms CD630_19090 - eutP Type: Gene Product:Ethanolamine utilization protein, GTPase family \| Pathway: \| COG: Amino acid transport and metabolism CD630_19210 - Type: Gene Product:Putative ethanolamine utilization protein \| Pathway: \| COG: Function unknown CD630_19070 - eutG Type: Gene Product:Ethanolamine iron-dependent Alcoholdehydrogenase \| Pathway: \| COG: Energy production and conversion CD630_19180 - eutM Type: Gene Product:Ethanolamine carboxysome structural protein, BMCfamily \| Pathway: \| COG: Amino acid transport and metabolism CD630_19140 - eutC Type: Gene Product:Ethanolamine ammonia lyase small subunit \| Pathway: Amine and polyamine degradation \| COG: Amino acid transport and metabolism CD630_19220 - eutN Type: Gene Product:Ethanolamine carboxysome structural protein, BMCfamily \| Pathway: \| COG: Amino acid transport and metabolism CD630_19150 - eutL Type: Gene Product:Ethanolamine carboxysome structural protein, BMCfamily \| Pathway: \| COG: Amino acid transport and metabolism	1.8	`NA`	0.21	Inferelator: 1 Hypergeometric: 1 TF Influences from Inferelator CD630_19100 - eutV Type: Gene Product:Two-component response regulator, Ethanolaminespecific \| Pathway: \| COG: Signal transduction mechanisms TF Influences from Hypergeometric Test CD630_32450 - prdR Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription
Module_78	19 CD630_25270 - Type: Gene Product:Transcriptional regulator, TetR family \| Pathway: \| COG: Transcription CD630_36590 - Type: Gene Product:Putative signal transduction phosphoesterase \| Pathway: \| COG: Signal transduction mechanisms CD630_25280 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_02990 - rbsK Type: Gene Product:Ribokinase, pfkB family \| Pathway: Carbohydrate metabolism \| COG: Carbohydrate transport and metabolism CD630_36620 - ssb Type: Gene Product:Single-stranded DNA-binding protein(Helix-destabilizing protein) \| Pathway: \| COG: Replication, recombination and repair CD630_36570 - dnaB Type: Gene Product:Replicative DNA helicase \| Pathway: \| COG: Replication, recombination and repair CD630_36610 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_36611 - rpsR Type: Gene Product:30S ribosomal protein S18 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_03000 - rbsB Type: Gene Product:ABC-type transport system, ribose-specificextracellular solute-binding protein \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_03290 - Type: Gene Product:Putative aminopeptidase I, M18 family \| Pathway: \| COG: Amino acid transport and metabolism CD630_36630 - rpsF Type: Gene Product:30S ribosomal protein S6 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_02980 - rbsR Type: Gene Product:Transcriptional regulator, LacI family \| Pathway: \| COG: Transcription CD630_36600 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_03010 - rbsA Type: Gene Product:ABC-type transport system, ribose-specificATP-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_36580 - rplI Type: Gene Product:50S ribosomal protein L9 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_03300 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_03280 - pcrA Type: Gene Product:DNA helicase, UvrD/REP type \| Pathway: \| COG: Replication, recombination and repair CD630_03020 - rbsC Type: Gene Product:ABC-type transport system, ribose-specificpermease \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_03310 - ppiB Type: Gene Product:Peptidyl-prolyl cis-trans isomerase B (PPIase B)(Rotamase B) \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones	0.13	`NA`	0.53	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_02980 - rbsR Type: Gene Product:Transcriptional regulator, LacI family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_350	22 CD630_10600 - Type: Gene Product:Putative pseudouridylate synthase \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_08850 - glgP Type: Gene Product:Glycogen phosphorylase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_10540 - bcd2 Type: Gene Product:Butyryl-CoA dehydrogenase \| Pathway: \| COG: Lipid transport and metabolism CD630_10560 - etfA Type: Gene Product:Electron transfer flavoprotein subunit alpha \| Pathway: \| COG: Energy production and conversion CD630_16550 - Type: Gene Product:Putative Na+/H+ antiporter NhaC-like \| Pathway: \| COG: Energy production and conversion CD630_10580 - hbd Type: Gene Product:3-hydroxybutyryl-CoA dehydrogenase \| Pathway: \| COG: Lipid transport and metabolism CD630_17750 - Type: Gene Product:ABC-type transport system, aminoacid-familypermease \| Pathway: \| COG: Amino acid transport and metabolism CD630_25370 - Type: Gene Product:Putative membrane-associated5'-nucleotidase/phosphoesterase \| Pathway: \| COG: Nucleotide transport and metabolism CD630_08840 - glgA Type: Gene Product:Glycogen synthase (Starch [bacterial glycogen]synthase) \| Pathway: Glycan biosynthesis \| COG: Carbohydrate transport and metabolism CD630_08860 - Type: Gene Product:Putative alpha-amylase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_10550 - etfB Type: Gene Product:Electron transfer flavoproteins subunit beta \| Pathway: \| COG: Energy production and conversion CD630_31450 - cbpA Type: Gene Product:Surface-exposed adhesin \| Pathway: \| COG: Function unknown CD630_10610 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_28320 - Type: Gene Product:Putative cation efflux protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_10570 - crt2 Type: Gene Product:3-hydroxybutyryl-CoA dehydratase (Crotonase) \| Pathway: \| COG: Lipid transport and metabolism CD630_08830 - glgD Type: Gene Product:Glycogen biosynthesis protein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_10590 - thlA1 Type: Gene Product:Acetoacetyl-CoA thiolase 1 \| Pathway: Metabolic intermediate biosynthesis \| COG: Lipid transport and metabolism CD630_21900 - Type: Gene Product:Cyclomaltodextrinase (maltogenic alpha-amylase)(cyclomaltodextrin dextrin-hydrolase (decyclizing)) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_17740 - Type: Gene Product:ABC-type transport system, aminoacid-familyextracellular solute-binding protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_25030 - Type: Gene Product:Putative cation-transporting P-type ATPase \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_15230 - Type: Gene Product:Putative transporter \| Pathway: \| COG: Function unknown CD630_17760 - Type: Gene Product:ABC-type transport system, aminoacid-familyATP-binding protein \| Pathway: \| COG: Amino acid transport and metabolism	0.00000000000026	`NA`	0.61	Inferelator: 2 Hypergeometric: 3 TF Influences from Inferelator CD630_05160 - Type: Gene Product:Transcription antiterminator \| Pathway: \| COG: Signal transduction mechanisms CD630_29800 - Type: Gene Product:Putative CRISPR-associated autoregulator DevRfamily protein protein \| Pathway: \| COG: Replication, recombination and repair TF Influences from Hypergeometric Test CD630_12750 - codY Type: Gene Product:Transcriptional regulator, GTP-sensingpleiotropic repressor \| Pathway: \| COG: Transcription CD630_32450 - prdR Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription CD630_10640 - ccpA Type: Gene Product:Transcriptional regulator, LacI family \| Pathway: \| COG: Transcription
Module_238	9 CD630_06000 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Transcription CD630_17291 - Type: Gene Product:Fragment of putative transcriptional regulator,AraC family (C-terminal region) \| Pathway: \| COG: Signal transduction mechanisms CD630_22250 - Type: Gene Product:Fragment of putative integrase (N-terminalregion) \| Pathway: \| COG: Replication, recombination and repair CD630_12360 - Type: Gene Product:Fragment of putative phage protein (part 1) \| Pathway: \| COG: CD630_30200 - Type: Gene Product:Fragment of conserved hypothetical protein,DUF1848 family (Part 2) \| Pathway: \| COG: Function unknown CD630_23060 - Type: Gene Product:Fragment of putative tranposase (Central region) \| Pathway: \| COG: CD630_11140 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn4-Orf5 \| Pathway: \| COG: CD630_29721 - Type: Gene Product:Fragment of conserved hypothetical protein(Central region) \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_01820 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG:	`NA`	`NA`	0.45	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_36460 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_94	5 CD630_14240 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_18800 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_31580 - Type: Gene Product:Transcriptional regulator, TRAP family \| Pathway: \| COG: Function unknown CD630_06580 - cdu1 Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription CD630_27880 - Type: Gene Product:Putative membrane protein, GtrA family \| Pathway: \| COG: Function unknown	`NA`	`NA`	0.51	Inferelator: 3 Hypergeometric: 0 TF Influences from Inferelator CD630_06290 - Type: Gene Product:Transcriptional regulator, Crp family \| Pathway: \| COG: Transcription CD630_06580 - cdu1 Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription CD630_23900 - Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_366	16 CD630_22740 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_16781 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_09401 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_22750 - topB2 Type: Gene Product:DNA topoisomerase III \| Pathway: \| COG: Replication, recombination and repair CD630_t0240 - tRNA-Leu Type: Gene Product: \| Pathway: \| COG: CD630_11360 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_21840 - Type: Gene Product:Putative N-acetylmuramoyl-L-alanine amidase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_06840 - Type: Gene Product:Putative ATP-dependent peptidase, M41 family \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_17010 - recQ Type: Gene Product:ATP-dependent DNA helicase \| Pathway: \| COG: Replication, recombination and repair CD630_23460 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_20680 - Type: Gene Product:ABC drug efflux pump \| Pathway: \| COG: Function unknown CD630_16731 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_01960 - Type: Gene Product:Fragment of conserved hypothetical protein,DUF111 family (Part 1) \| Pathway: \| COG: Function unknown, Function unknown CD630_20021 - Type: Gene Product:Fragment of conserved hypothetical protein(N-terminal region) \| Pathway: \| COG: Function unknown	`NA`	`NA`	0.61	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_26400 - nrdR Type: Gene Product:Transcriptional regulator, repressor NrdR family \| Pathway: \| COG: Transcription CD630_34990 - spoVT Type: Gene Product:Stage V sporulation protein T \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_254	4 CD630_18430 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_02920 - Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription CD630_30070 - Type: Gene Product:Putative L,D-transpeptidases \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_29570 - ntpC Type: Gene Product:V-type sodium ATPase subunit C \| Pathway: \| COG: Energy production and conversion	`NA`	`NA`	0.54	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_25950 - pyrR Type: Gene Product:Bifunctional protein PyrR [Includes: Pyrimidineoperon regulatory protein; Uracil phosphoribosyltransferase(UPRTase)] \| Pathway: \| COG: Nucleotide transport and metabolism TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_382	17 CD630_00890 - rplO Type: Gene Product:50S ribosomal protein L15 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00840 - rplE Type: Gene Product:50S ribosomal protein L5 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00760 - rplB Type: Gene Product:50S ribosomal protein L2 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00730 - rplC Type: Gene Product:50S ribosomal protein L3 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00970 - rpsD Type: Gene Product:30S ribosomal protein S4 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_01020 - cbiQ Type: Gene Product:ABC-type transport system, cobalt-specificpermease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_00680 - rpsL Type: Gene Product:30S ribosomal protein S12 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00690 - rpsG Type: Gene Product:30S ribosomal protein S7 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00960 - rpsK Type: Gene Product:30S ribosomal protein S11 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00850 - rpsH Type: Gene Product:30S ribosomal protein S8 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_01000 - cbiO1 Type: Gene Product:ABC-type transport system, cobalt-specificATP-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_00800 - rplP Type: Gene Product:50S ribosomal protein L16 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00720 - rpsJ Type: Gene Product:30S ribosomal protein S10 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_01030 - truA1 Type: Gene Product:tRNA pseudouridine synthase A 1 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00910 - adk Type: Gene Product:Adenylate kinase \| Pathway: Purine metabolism \| COG: Nucleotide transport and metabolism CD630_t0860 - tRNA-Glu Type: Gene Product: \| Pathway: \| COG: CD630_01010 - cbiO2 Type: Gene Product:ABC-type transport system, cobalt-specificATP-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism	`NA`	`NA`	0.41	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_11770 - fapR Type: Gene Product:Transcriptional regulator, DeoR family (Fattyacid and phospholipid biosynthesis regulator) \| Pathway: \| COG: Transcription CD630_23830 - Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`