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 51 - 60 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_249	6 CD630_04371 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_07690 - Type: Gene Product:Putative oxidoreductase subunit \| Pathway: \| COG: Energy production and conversion CD630_13430 - glnA Type: Gene Product:Glutamine synthetase \| Pathway: \| COG: Amino acid transport and metabolism CD630_23030 - Type: Gene Product:Fragment of putative phage transcriptionalrepressor (N-terminal region) \| Pathway: \| COG: Transcription CD630_20470 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_06580 - cdu1 Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription	`NA`	`NA`	0.52	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_06580 - cdu1 Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_185	6 CD630_08670 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_08660 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_07141 - Type: Gene Product:Fragment of sugar O-acetyltransferase (C-terminalregion) \| Pathway: \| COG: Function unknown CD630_21670 - Type: Gene Product:Acyl transferase/acylhydrolase/lysophospholipase \| Pathway: \| COG: Function unknown CD630_12401 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_08790 - Type: Gene Product:Putative carbohydrate kinase \| Pathway: \| COG: Carbohydrate transport and metabolism	`NA`	`NA`	0.55	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_21430 - Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_345	18 CD630_29340 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_12690 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_15910 - kdpA Type: Gene Product:Potassium-translocating ATPase A chain \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_12700 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_15930 - kdpC Type: Gene Product:Potassium-transporting ATPase C chain \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_12740 - topA Type: Gene Product:DNA topoisomerase I \| Pathway: \| COG: Replication, recombination and repair CD630_12720 - Type: Gene Product:Putative magnesium chelatase \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_36320 - Type: Gene Product:Putative isochorismatase (2,3 dihydro-2,3dihydroxybenzoate synthase) \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_12760 - Type: Gene Product:Putative replication-associated recombinationprotein A RarA \| Pathway: \| COG: Replication, recombination and repair CD630_29330 - Type: Gene Product:Hypothetical protein \| Pathway: \| COG: CD630_29290 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_12750 - codY Type: Gene Product:Transcriptional regulator, GTP-sensingpleiotropic repressor \| Pathway: \| COG: Transcription CD630_29320 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_36330 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_29300 - Type: Gene Product:Putative phage anti-repressor protein \| Pathway: \| COG: Transcription CD630_12670 - Type: Gene Product:ABC-type transport system, multidrug-familypermease \| Pathway: \| COG: Function unknown CD630_12780 - iscR Type: Gene Product:Transcriptional regulator, Rrf2 family \| Pathway: \| COG: Transcription CD630_29310 - Type: Gene Product:Putative phage endodeoxyribonuclease RusA-like \| Pathway: \| COG: Replication, recombination and repair	`NA`	`NA`	0.48	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_22140 - SinR Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_218	19 CD630_04351 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn2-Orf32 \| Pathway: \| COG: CD630_04360 - Type: Gene Product:Putative recombinase Tn1549-like, CTn2-Orf34 \| Pathway: \| COG: Replication, recombination and repair CD630_21140 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_33722 - Type: Gene Product:Putative conjugative transposon proteinTn916-like, CTn7-Orf6 \| Pathway: \| COG: Function unknown CD630_21130 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms	`NA`	`NA`	0.49	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_21140 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_394	19 CD630_11130 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn4-Orf6 \| Pathway: \| COG: Function unknown CD630_22241 - Type: Gene Product:Putative extrachromosomal origin protein \| Pathway: \| COG: CD630_11042 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn4-Orf17 \| Pathway: \| COG: Function unknown CD630_11120 - Type: Gene Product:Putative membrane protein Tn1549-like, CTn4-Orf7 \| Pathway: \| COG: Function unknown CD630_11071 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn4-Orf12 \| Pathway: \| COG: Function unknown CD630_11070 - Type: Gene Product:Putative cell surface protein Tn1549-like,CTn4-Orf13 \| Pathway: \| COG: Function unknown CD630_10540 - bcd2 Type: Gene Product:Butyryl-CoA dehydrogenase \| Pathway: \| COG: Lipid transport and metabolism CD630_10550 - etfB Type: Gene Product:Electron transfer flavoproteins subunit beta \| Pathway: \| COG: Energy production and conversion CD630_10560 - etfA Type: Gene Product:Electron transfer flavoprotein subunit alpha \| Pathway: \| COG: Energy production and conversion CD630_10580 - hbd Type: Gene Product:3-hydroxybutyryl-CoA dehydrogenase \| Pathway: \| COG: Lipid transport and metabolism CD630_10570 - crt2 Type: Gene Product:3-hydroxybutyryl-CoA dehydratase (Crotonase) \| Pathway: \| COG: Lipid transport and metabolism CD630_10590 - thlA1 Type: Gene Product:Acetoacetyl-CoA thiolase 1 \| Pathway: Metabolic intermediate biosynthesis \| COG: Lipid transport and metabolism CD630_11050 - Type: Gene Product:Putative antirestriction protein Tn1549-like,CTn4-Orf16 \| Pathway: \| COG: Function unknown CD630_11080 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn4-Orf11 \| Pathway: \| COG: Function unknown CD630_11090 - Type: Gene Product:DNA-methyltransferase, cytosine-N4-specific;Tn1549-like, CTn4-Orf10 \| Pathway: \| COG: Replication, recombination and repair CD630_11110 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn4-Orf8 \| Pathway: \| COG: Function unknown CD630_11061 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn4-Orf14 \| Pathway: \| COG: Function unknown CD630_11060 - topB Type: Gene Product:DNA topoisomerase III; Tn1549-like, CTn4-Orf15 \| Pathway: \| COG: Replication, recombination and repair CD630_11100 - Type: Gene Product:Putative hydrolase Tn1549-like, CTn4-Orf9 \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport	`NA`	`NA`	0.45	Inferelator: 0 Hypergeometric: 3 TF Influences from Inferelator `No TF influences from Inferelator` 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_96	6 CD630_12870 - fur Type: Gene Product:Transcriptional regulator, Fur family \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_31470 - Type: Gene Product:Putative DNA-methyltransferase \| Pathway: \| COG: Replication, recombination and repair CD630_36340 - Type: Gene Product:Transcriptional regulator, MerR family \| Pathway: \| COG: Transcription CD630_09740 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_29640 - Type: Gene Product:Putative tRNA-binding protein \| Pathway: \| COG: Function unknown CD630_05320 - Type: Gene Product:Putative transcriptional regulator \| Pathway: \| COG: Transcription	`NA`	`NA`	0.57	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_05320 - Type: Gene Product:Putative transcriptional regulator \| Pathway: \| COG: Transcription CD630_12870 - fur Type: Gene Product:Transcriptional regulator, Fur family \| Pathway: \| COG: Inorganic ion transport and metabolism TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_202	6 CD630_17720 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_26040 - Type: Gene Product:Fragment of ADP-ribosyltransferase CdtAB (Part1) \| Pathway: \| COG: CD630_28240 - Type: Gene Product:Fragment of putative membrane protein (C-terminalregion) \| Pathway: \| COG: Function unknown CD630_33810 - Type: Gene Product:Fragment of putative membrane protein Tn916-like,CTn7-orf17 (Part 2) \| Pathway: \| COG: Function unknown, Function unknown CD630_32210 - Type: Gene Product:Putative peptidase, M20D family \| Pathway: \| COG: Amino acid transport and metabolism CD630_18130 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown	`NA`	`NA`	0.53	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_17250 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_1	18 CD630_12170 - Type: Gene Product:Putative glycosyl transferase, family 2 \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_12230 - drm Type: Gene Product:Phosphopentomutase (Phosphodeoxyribomutase) \| Pathway: Metabolic intermediate biosynthesis \| COG: Carbohydrate transport and metabolism CD630_12200 - nudF Type: Gene Product:Putative hydrolase, NUDIX family \| Pathway: \| COG: Nucleotide transport and metabolism CD630_12250 - pdp Type: Gene Product:Pyrimidine-nucleoside phosphorylase \| Pathway: \| COG: Nucleotide transport and metabolism CD630_36590 - Type: Gene Product:Putative signal transduction phosphoesterase \| Pathway: \| COG: Signal transduction mechanisms CD630_12160 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_12240 - pupG Type: Gene Product:Purine nucleoside phosphorylase \| Pathway: Purine metabolism \| COG: Nucleotide transport and metabolism CD630_12180 - Type: Gene Product:Putative glycosyl transferase \| Pathway: \| COG: Function unknown CD630_12190 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_36570 - dnaB Type: Gene Product:Replicative DNA helicase \| Pathway: \| COG: Replication, recombination and repair CD630_12220 - Type: Gene Product:Putative phage integrase site-specificrecombinase XerD-like \| Pathway: \| COG: Replication, recombination and repair CD630_36610 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_12150 - Type: Gene Product:Putative pyrophosphokinase, DUF115 family \| Pathway: \| COG: Function unknown CD630_12210 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_36630 - rpsF Type: Gene Product:30S ribosomal protein S6 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_36620 - ssb Type: Gene Product:Single-stranded DNA-binding protein(Helix-destabilizing protein) \| Pathway: \| COG: Replication, recombination and repair CD630_36580 - rplI Type: Gene Product:50S ribosomal protein L9 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_36611 - rpsR Type: Gene Product:30S ribosomal protein S18 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis	`NA`	`NA`	0.46	Inferelator: 1 Hypergeometric: 1 TF Influences from Inferelator CD630_05590 - Type: Gene Product:Transcriptional regulator, ArsR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_12140 - spo0A Type: Gene Product:Stage 0 sporulation protein A \| Pathway: \| COG: Signal transduction mechanisms
Module_364	10 CD630_25010 - Type: Gene Product:Putative hydrolase, HAD superfamily, IIBsubfamily \| Pathway: \| COG: Function unknown CD630_22951 - Type: Gene Product:Fragment of putative cell surface protein(C-terminal region) \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_24990 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_22190 - Type: Gene Product:Fragment of conjugative transposon protein(central region) \| Pathway: \| COG: Function unknown CD630_06071 - Type: Gene Product:Fragment of transposase-like protein B(C-terminal region) \| Pathway: \| COG: Replication, recombination and repair CD630_18090 - Type: Gene Product:Fragment of putative permease, MFS family (Part1) \| Pathway: \| COG: Carbohydrate transport and metabolism, Carbohydrate transport and metabolism CD630_30310 - Type: Gene Product:Transcription antiterminator, PTS operonregulator \| Pathway: \| COG: Transcription CD630_19440 - Type: Gene Product:Fragment of conserved hypothetical protein(C-terminal region) \| Pathway: \| COG: Function unknown CD630_33911 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG:	`NA`	`NA`	0.58	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_26650 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_31750 - cggR Type: Gene Product:Transcriptional regulator, SorC family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_300	4 CD630_05500 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_08600 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_06330 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Replication, recombination and repair CD630_05760 - virS Type: Gene Product:Sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms	`NA`	`NA`	0.47	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_27300 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`