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 21 - 30 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_147	21 CD630_03960 - hadI Type: Gene Product:Activator of 2-hydroxyisocaproyl-CoA dehydratase \| Pathway: \| COG: Lipid transport and metabolism CD630_04010 - etfA1 Type: Gene Product:Alpha-subunit of electron transfer flavoprotein \| Pathway: \| COG: Energy production and conversion CD630_11780 - plsX Type: Gene Product:Fatty acid/phospholipid synthesis protein PlsX \| Pathway: Lipid metabolism \| COG: Lipid transport and metabolism CD630_11800 - fabK Type: Gene Product:Enoyl-(Acyl-carrier-protein) reductase II \| Pathway: \| COG: Lipid transport and metabolism CD630_03950 - hadA Type: Gene Product:Isocaprenoyl-CoA:2-hydroxyisocaproateCoA-transferase \| Pathway: \| COG: Energy production and conversion CD630_11770 - fapR Type: Gene Product:Transcriptional regulator, DeoR family (Fattyacid and phospholipid biosynthesis regulator) \| Pathway: \| COG: Transcription CD630_11810 - fabD Type: Gene Product:Malonyl CoA-acyl carrier protein transacylase(MCT) \| Pathway: \| COG: Lipid transport and metabolism CD630_11790 - fabH Type: Gene Product:3-oxoacyl-[acyl-carrier-protein] synthase 3 \| Pathway: Lipid metabolism \| COG: Lipid transport and metabolism CD630_03990 - acdB Type: Gene Product:Acyl-CoA dehydrogenase, short-chain specific \| Pathway: \| COG: Lipid transport and metabolism CD630_00941 - rpmJ Type: Gene Product:50S ribosomal protein L36 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_09231 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_00881 - rpmD Type: Gene Product:50S ribosomal protein L30 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_03980 - hadC Type: Gene Product:Subunit of oxygen-sensitive2-hydroxyisocaproyl-CoA dehydratase C \| Pathway: \| COG: Amino acid transport and metabolism CD630_11840 - fabF Type: Gene Product:3-oxoacyl-[acyl-carrier-protein] synthase 2 \| Pathway: Lipid metabolism \| COG: Lipid transport and metabolism CD630_00841 - rpsZ Type: Gene Product:30S ribosomal protein S14 type Z \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_11820 - fabG Type: Gene Product:3-oxoacyl-[acyl-carrier protein] reductase(3-ketoacyl-acyl carrier protein reductase) \| Pathway: Lipid metabolism \| COG: Function unknown CD630_11830 - acpP Type: Gene Product:Acyl carrier protein (ACP) \| Pathway: Lipid metabolism \| COG: Lipid transport and metabolism CD630_03970 - hadB Type: Gene Product:Subunit of oxygen-sensitive2-hydroxyisocaproyl-CoA dehydratase B \| Pathway: \| COG: Amino acid transport and metabolism CD630_04000 - etfB1 Type: Gene Product:Beta-subunit of electron transfer flavoprotein \| Pathway: \| COG: Energy production and conversion CD630_00710 - tuf Type: Gene Product:Elongation factor EFTu/EF1A (EF-Tu) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00801 - rpmC Type: Gene Product:50S ribosomal protein L29 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis	`NA`	`NA`	0.34	Inferelator: 2 Hypergeometric: 1 TF Influences from Inferelator CD630_16930 - Type: Gene Product:Putative dinitrogenase iron-molybdenum cofactor \| Pathway: \| COG: Function unknown CD630_23900 - Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_31760 - glnF Type: Gene Product:RNA polymerase sigma-54 factor \| Pathway: \| COG: Transcription
Module_67	16 CD630_32780 - Type: Gene Product:PTS system, mannose/fructose/sorbose IIAcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_04480 - orr Type: Gene Product:ornithine racemase \| Pathway: \| COG: Amino acid transport and metabolism CD630_32790 - Type: Gene Product:PTS system, mannose/fructose/sorbose IIBcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_32760 - Type: Gene Product:PTS system, mannose/fructose/sorbose IIDcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_04490 - Type: Gene Product:Na+/H+ antiporter, NhaA family \| Pathway: \| COG: Energy production and conversion CD630_04440 - ortB Type: Gene Product:2-amino-4-ketopentanoate thiolase beta subunit \| Pathway: \| COG: Function unknown CD630_32750 - Type: Gene Product:Putative phosphosugar isomerase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_04420 - ord Type: Gene Product:2,4-diaminopentanoate dehydrogenase \| Pathway: \| COG: Amino acid transport and metabolism CD630_32770 - Type: Gene Product:PTS system, mannose/fructose/sorbose IICcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_31260 - bglG Type: Gene Product:Transcription antiterminator, PTS operonregulator \| Pathway: \| COG: Transcription CD630_04430 - ortA Type: Gene Product:2-amino-4-ketopentanoate thiolase alpha subunit \| Pathway: \| COG: Function unknown CD630_04460 - oraE Type: Gene Product:D-ornithine aminomutase E component \| Pathway: \| COG: Function unknown CD630_04470 - Type: Gene Product:Putative reactivating factor foradenosylcobalamine-dependent D-ornithine aminomutase \| Pathway: \| COG: Function unknown CD630_31240 - bglA Type: Gene Product:6-phospho-beta-glucosidase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_04450 - oraS Type: Gene Product:D-ornithine aminomutase S component \| Pathway: \| COG: Function unknown CD630_31250 - bglF Type: Gene Product:PTS system, beta-glucoside-specific IIABCcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism	`NA`	`NA`	0.27	Inferelator: 1 Hypergeometric: 1 TF Influences from Inferelator CD630_26430 - sigE Type: Gene Product:RNA polymerase sigma-E factor \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_12750 - codY Type: Gene Product:Transcriptional regulator, GTP-sensingpleiotropic repressor \| Pathway: \| COG: Transcription
Module_68	4 CD630_12910 - dacF Type: Gene Product:D-alanyl-D-alanine carboxypeptidase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_12900 - Type: Gene Product:Putative small acid-soluble spore protein SASP \| Pathway: \| COG: CD630_07080 - pepD Type: Gene Product:Peptidase D, aminoacyl-histidine dipeptidase \| Pathway: \| COG: Amino acid transport and metabolism CD630_32220 - sdaB Type: Gene Product:L-serine dehydratase \| Pathway: \| COG: Amino acid transport and metabolism	`NA`	`NA`	0.50	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_06290 - Type: Gene Product:Transcriptional regulator, Crp family \| Pathway: \| COG: Transcription CD630_25990 - Type: Gene Product:Putative transcriptional regulator \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_400	19 CD630_01170 - Type: Gene Product:Putative ferredoxin/flavodoxin oxidoreductase,beta subunit \| Pathway: \| COG: Energy production and conversion CD630_21360 - uppS Type: Gene Product:Undecaprenyl pyrophosphate synthetase \| Pathway: \| COG: Lipid transport and metabolism CD630_21361 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_01160 - Type: Gene Product:Putative ferredoxin/flavodoxin oxidoreductase,alpha subunit \| Pathway: \| COG: Energy production and conversion CD630_01180 - Type: Gene Product:Putative ferredoxin/flavodoxin oxidoreductase,gamma subunit \| Pathway: \| COG: Energy production and conversion CD630_01140 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_24460 - Type: Gene Product:Putative aspartyl/glutamyl-tRNA amidotransferasesubunit B-related \| Pathway: \| COG: Function unknown CD630_21350 - cdsA Type: Gene Product:Phosphatidate cytidylyltransferase CdsA \| Pathway: Phospholipid metabolism \| COG: Lipid transport and metabolism CD630_01120 - ptb Type: Gene Product:phosphate butyryltransferase \| Pathway: \| COG: Energy production and conversion CD630_21370 - frr Type: Gene Product:Ribosome-recycling factor \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_01150 - Type: Gene Product:Putative 4Fe-4S ferredoxin, iron-sulfur bindingdomain protein, delta subunit \| Pathway: \| COG: Energy production and conversion CD630_34740 - atpB Type: Gene Product:ATP synthase subunit a \| Pathway: \| COG: Energy production and conversion CD630_01190 - glmM Type: Gene Product:Phosphoglucosamine mutase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_34720 - atpF Type: Gene Product:ATP synthase subunit b \| Pathway: \| COG: Energy production and conversion CD630_01130 - buk Type: Gene Product:Butyrate kinase (BK) (Branched-chain carboxylicacid kinase) \| Pathway: \| COG: Energy production and conversion CD630_34760 - atpZ Type: Gene Product:ATP synthase transporter \| Pathway: \| COG: Function unknown CD630_34670 - atpC Type: Gene Product:ATP synthase epsilon chain \| Pathway: \| COG: Energy production and conversion CD630_21400 - rpsB Type: Gene Product:30S ribosomal protein S2 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_21950 - ftnA Type: Gene Product:Ferritin \| Pathway: \| COG: Inorganic ion transport and metabolism	`NA`	`NA`	0.32	Inferelator: 4 Hypergeometric: 0 TF Influences from Inferelator CD630_16920 - Type: Gene Product:Transcriptional regulator, ArsR family \| Pathway: \| COG: Transcription CD630_16930 - Type: Gene Product:Putative dinitrogenase iron-molybdenum cofactor \| Pathway: \| COG: Function unknown CD630_22200 - Type: Gene Product:Putative cyclic nucleotides-binding protein \| Pathway: \| COG: Signal transduction mechanisms 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_116	6 CD630_06740 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_13380 - Type: Gene Product:Putative 6-phospho-beta-glucosidase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_07141 - Type: Gene Product:Fragment of sugar O-acetyltransferase (C-terminalregion) \| Pathway: \| COG: Function unknown CD630_13370 - Type: Gene Product:Transcriptional regulator, RpiR family \| Pathway: \| COG: Transcription CD630_06050 - Type: Gene Product:Fragment of conserved hypothetical protein(N-terminal region) \| Pathway: \| COG: Function unknown	`NA`	`NA`	0.55	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_13370 - Type: Gene Product:Transcriptional regulator, RpiR family \| Pathway: \| COG: Transcription 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_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_101	12 CD630_03480 - Type: Gene Product:Fragment of conserved hypothetical protein (Part1) \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism, Secondary metabolites biosynthesis, transport and catabolism CD630_05071 - Type: Gene Product:Fragment of Tet(M) leader peptide Tn5397,CTn3-orf12 (C-terminal region) \| Pathway: \| COG: CD630_13880 - Type: Gene Product:Fragment of trancriptional regulator (Part 2) \| Pathway: \| COG: Transcription CD630_20052 - Type: Gene Product:Fragment of conserved hypothetical protein(Central region) \| Pathway: \| COG: Function unknown CD630_08580 - Type: Gene Product:Fragment of transcriptional regulator,sigma-54-dependent (Part 1), PRD domain \| Pathway: \| COG: Signal transduction mechanisms, Signal transduction mechanisms CD630_33580 - Type: Gene Product:Fragment of C-terminal transcriptional regulator,AsnC/Lrp family \| Pathway: \| COG: Transcription CD630_24591 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_06780 - Type: Gene Product:Fragment of conserved hypothetical protein(C-terminal region) \| Pathway: \| COG: CD630_36740 - rsmG Type: Gene Product:Fragment of 7-methylguanosine methyltransferasespecific for the 16S rRNA (Part 2) \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis, Cell wall/membrane/envelope biogenesis CD630_22210 - Type: Gene Product:Fragment of putative extrachromosomal protein(C-terminal region) \| Pathway: \| COG: Function unknown	`NA`	`NA`	0.47	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_70	23 CD630_29550 - ntpB Type: Gene Product:V-type sodium ATPase subunit B \| Pathway: \| COG: Energy production and conversion CD630_29610 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_32530 - folC Type: Gene Product:Folylpolyglutamate synthase \| Pathway: \| COG: Coenzyme transport and metabolism CD630_33690 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_35440 - Type: Gene Product:Transcriptional regulator, AsnC/Lrp family \| Pathway: \| COG: Transcription CD630_29590 - ntpK Type: Gene Product:V-type sodium ATPase subunit K \| Pathway: \| COG: Energy production and conversion CD630_29980 - Type: Gene Product:ABC-type transport system, iron-family permease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_09240 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_16450 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_29600 - ntpI Type: Gene Product:V-type sodium ATPase subunit I \| Pathway: \| COG: Energy production and conversion CD630_01480 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_29540 - ntpD Type: Gene Product:V-type sodium ATPase subunit D \| Pathway: \| COG: Energy production and conversion CD630_29560 - ntpA Type: Gene Product:V-type sodium ATPase subunit A \| Pathway: \| COG: Energy production and conversion CD630_29561 - ntpF Type: Gene Product:V-type sodium ATPase subunit F \| Pathway: \| COG: Energy production and conversion CD630_29580 - ntpE Type: Gene Product:V-type sodium ATPase subunit E \| Pathway: \| COG: Energy production and conversion CD630_29970 - Type: Gene Product:ABC-type transport system, iron-familyATP-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_23010 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_29990 - Type: Gene Product:ABC-type transport system, iron-familyextracellular solute-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_32800 - Type: Gene Product:Sigma-54 dpendent regulator, PTS fructose family \| Pathway: \| COG: Signal transduction mechanisms CD630_35430 - Type: Gene Product:Putative nicotinate phosphribosyltransferase \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_16460 - Type: Gene Product:Putative peptidase, M19 family \| Pathway: \| COG: Amino acid transport and metabolism CD630_16440 - Type: Gene Product:Transcriptional regulator, RmlC-type \| Pathway: \| COG: Transcription CD630_20451 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG:	`NA`	`NA`	0.56	Inferelator: 2 Hypergeometric: 2 TF Influences from Inferelator CD630_16050 - Type: Gene Product:Putative transcriptional regulator \| Pathway: \| COG: Transcription CD630_20480 - Type: Gene Product:Transcriptional regulator, RpiR family \| Pathway: \| COG: Transcription 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
Module_252	4 CD630_21341 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_07390 - Type: Gene Product:Putative exported protein \| Pathway: \| COG: CD630_12340 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_18440 - Type: Gene Product:Fragment of conserved hypothetical protein (Part1) \| Pathway: \| COG: Function unknown	`NA`	`NA`	0.29	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_13810 - Type: Gene Product:Transcriptional regulator, TetR family \| Pathway: \| COG: Transcription CD630_16880 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`