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 81 - 90 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_383	9 CD630_32690 - Type: Gene Product:Putative oligoendopeptidase F, M3B family \| Pathway: \| COG: Amino acid transport and metabolism CD630_31560 - Type: Gene Product:phage integrase \| Pathway: \| COG: Replication, recombination and repair CD630_19902 - cspC Type: Gene Product:Major cold shock protein CspC \| Pathway: \| COG: Transcription CD630_13950 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_32700 - Type: Gene Product:Putative magnesium transport ATPase, MgtC/SapBfamily \| Pathway: \| COG: Function unknown CD630_18080 - Type: Gene Product:Pyridoxal-dependent decarboxylase, group IVdecarboxylase family \| Pathway: \| COG: Amino acid transport and metabolism CD630_23100 - cspD Type: Gene Product:Cold shock protein D \| Pathway: \| COG: Transcription CD630_18070 - Type: Gene Product:Putative NADPH-dependent FMN reductase \| Pathway: \| COG: Function unknown CD630_12341 - Type: Gene Product:Putative phage protein \| Pathway: \| COG:	`NA`	`NA`	0.65	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_05590 - Type: Gene Product:Transcriptional regulator, ArsR family \| Pathway: \| COG: Transcription CD630_19100 - eutV Type: Gene Product:Two-component response regulator, Ethanolaminespecific \| Pathway: \| COG: Signal transduction mechanisms TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_26	6 CD630_07570 - Type: Gene Product:Phosphodiesterases protein \| Pathway: \| COG: Signal transduction mechanisms CD630_18311 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_20160 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_18430 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_10150 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms	`NA`	`NA`	0.49	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_399	18 CD630_26200 - Type: Gene Product:Putative RNA-binding cell division protein \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_26190 - Type: Gene Product:Putative cell-division initiation protein DivIVA \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning CD630_26210 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_01940 - groL Type: Gene Product:60 kDa chaperonin (Protein Cpn60) (GroELprotein) \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_26230 - Type: Gene Product:Putative pyridoxal 5'-phosphate-dependent enzyme \| Pathway: \| COG: Nucleotide transport and metabolism CD630_19390 - accB Type: Gene Product:Acetyl-CoA carboxylase subunit \| Pathway: Lipid metabolism \| COG: Lipid transport and metabolism CD630_19380 - accC Type: Gene Product:Acetyl-CoA carboxylase subunit \| Pathway: Lipid metabolism \| COG: Lipid transport and metabolism CD630_19370 - accD Type: Gene Product:Acetyl-CoA carboxylase subunit beta \| Pathway: Lipid metabolism \| COG: Lipid transport and metabolism CD630_01930 - groS Type: Gene Product:10 kDa chaperonin (Protein Cpn10) (GroESprotein) \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_34740 - atpB Type: Gene Product:ATP synthase subunit a \| Pathway: \| COG: Energy production and conversion CD630_34720 - atpF Type: Gene Product:ATP synthase subunit b \| Pathway: \| COG: Energy production and conversion CD630_34730 - atpE Type: Gene Product:ATP synthase subunit c \| 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_26220 - sepF Type: Gene Product:Cell division protein SepF \| Pathway: \| COG: Function unknown CD630_26240 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_34750 - atpI Type: Gene Product:ATP synthase subunit I \| Pathway: \| COG: Function unknown CD630_19360 - accA Type: Gene Product:Acetyl-coenzyme A carboxylase carboxyltransferase subunit alpha \| Pathway: Lipid metabolism \| COG: Lipid transport and metabolism	`NA`	`NA`	0.26	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_17820 - 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_139	24 CD630_29340 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_18360 - pheA Type: Gene Product:Bifunctional P-protein, chorismatemutase/prephenate dehydratase \| Pathway: \| COG: Amino acid transport and metabolism CD630_18340 - aroA Type: Gene Product:3-phosphoshikimate 1-carboxyvinyltransferase \| Pathway: Metabolic intermediate biosynthesis \| COG: Amino acid transport and metabolism CD630_15490 - hisC Type: Gene Product:Histidinol-phosphate aminotransferase (Imidazoleacetol-phosphate transaminase) \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_15510 - hisH Type: Gene Product:Imidazole glycerol phosphate synthase subunitHisH \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_15530 - hisF Type: Gene Product:Imidazole glycerol phosphate synthase subunitHisF \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_15470 - hisZ Type: Gene Product:ATP phosphoribosyltransferase regulatory subunit \| Pathway: \| COG: Amino acid transport and metabolism CD630_18390 - tyrC Type: Gene Product:Prephenate dehydrogenase \| Pathway: \| COG: Amino acid transport and metabolism CD630_29330 - Type: Gene Product:Hypothetical protein \| Pathway: \| COG: CD630_18330 - aroB Type: Gene Product:3-dehydroquinate synthase \| Pathway: Metabolic intermediate biosynthesis \| COG: Amino acid transport and metabolism CD630_29310 - Type: Gene Product:Putative phage endodeoxyribonuclease RusA-like \| Pathway: \| COG: Replication, recombination and repair CD630_18350 - aroC Type: Gene Product:Chorismate synthase(5-enolpyruvylshikimate-3-phosphate phospholyase) \| Pathway: Metabolic intermediate biosynthesis \| COG: Amino acid transport and metabolism CD630_15480 - hisG Type: Gene Product:ATP phosphoribosyltransferase (ATP-PRTase)(ATP-PRT) \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_18370 - aroE1 Type: Gene Product:Shikimate dehydrogenase 1 \| Pathway: Metabolic intermediate biosynthesis \| COG: Amino acid transport and metabolism CD630_29290 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_15540 - hisI Type: Gene Product:Histidine biosynthesis bifunctional protein HisIE[Includes: Phosphoribosyl-AMP cyclohydrolase ;Phosphoribosyl-ATP pyrophosphatase] \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_15520 - hisA Type: Gene Product:1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_18380 - aroK Type: Gene Product:Shikimate kinase (SK) \| Pathway: Metabolic intermediate biosynthesis \| COG: Amino acid transport and metabolism CD630_15500 - hisB Type: Gene Product:Imidazoleglycerol-phosphate dehydratase \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_29320 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_29300 - Type: Gene Product:Putative phage anti-repressor protein \| Pathway: \| COG: Transcription CD630_18320 - aroF Type: Gene Product:3-deoxy-D-arabino-heptulosonate 7-phosphatesynthase \| Pathway: \| COG: Amino acid transport and metabolism	`NA`	`NA`	0.58	Inferelator: 3 Hypergeometric: 1 TF Influences from Inferelator CD630_19960 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Signal transduction mechanisms CD630_26150 - Type: Gene Product:Transcriptional regulator, TetR family \| Pathway: \| COG: Transcription CD630_32090 - Type: Gene Product:Transcriptional regulator, PadR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_12750 - codY Type: Gene Product:Transcriptional regulator, GTP-sensingpleiotropic repressor \| Pathway: \| COG: Transcription
Module_75	12 CD630_16632 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_35871 - Type: Gene Product:Fragment of putative transposase (N-terminalregion) \| Pathway: \| COG: CD630_34400 - Type: Gene Product:Putative glycoside hydrolase-typecarbohydrate-binding protein \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_06012 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_23020 - tlpB Type: Gene Product:Fragment of transposase-like protein B(C-terminal region) \| Pathway: \| COG: Replication, recombination and repair CD630_04370 - Type: Gene Product:Fragment of integrase Tn1549-like, CTn2(C-terminal region) \| Pathway: \| COG: Replication, recombination and repair CD630_18110 - Type: Gene Product:Fragment of putative two-component sensorhistidine kinase (N-terminal region) \| Pathway: \| COG: Signal transduction mechanisms CD630_29721 - Type: Gene Product:Fragment of conserved hypothetical protein(Central region) \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_21450 - Type: Gene Product:DNA mismatch repair protein \| Pathway: \| COG: Replication, recombination and repair CD630_21930 - cwp24 Type: Gene Product:Putative cell wall-binding protein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_01820 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_06050 - Type: Gene Product:Fragment of conserved hypothetical protein(N-terminal region) \| Pathway: \| COG: Function unknown	`NA`	`NA`	0.47	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_26650 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_175	12 CD630_19904 - Type: Gene Product:Fragment of conserved hypothetical protein \| Pathway: \| COG: CD630_21710 - Type: Gene Product:Fragment of putative sodium:dicarboxylatesymporter (Part 2) \| Pathway: \| COG: Energy production and conversion, Energy production and conversion CD630_05102 - Type: Gene Product:Fragment of putative conjugative transposonprotein Tn5397, CTn3-Orf5 (C-terminal region) \| Pathway: \| COG: CD630_23011 - Type: Gene Product:Fragment of putative phage protein (C-terminalregion) \| Pathway: \| COG: CD630_09030 - Type: Gene Product:Fragment of putative oxydoreductase (Part 1) \| Pathway: \| COG: Energy production and conversion, Energy production and conversion CD630_33580 - Type: Gene Product:Fragment of C-terminal transcriptional regulator,AsnC/Lrp family \| Pathway: \| COG: Transcription CD630_14370 - Type: Gene Product:Fragment of transcriptional regulator,sigma-54-dependent (N-terminal region) \| Pathway: \| COG: Transcription CD630_33810 - Type: Gene Product:Fragment of putative membrane protein Tn916-like,CTn7-orf17 (Part 2) \| Pathway: \| COG: Function unknown, Function unknown CD630_08080 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_06780 - Type: Gene Product:Fragment of conserved hypothetical protein(C-terminal region) \| Pathway: \| COG: CD630_22840 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_17452 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG:	`NA`	`NA`	0.51	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_11	22 CD630_11480 - Type: Gene Product:Putative penicillin-binding protein with aN-terminal TonB-box \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_11510 - minE Type: Gene Product:Cell division topological specificity factor \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning CD630_01720 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Energy production and conversion CD630_13350 - Type: Gene Product:Transcriptional regulator, MarR family \| Pathway: \| COG: Transcription CD630_11440 - radC Type: Gene Product:DNA repair protein RadC homolog \| Pathway: \| COG: Replication, recombination and repair CD630_32990 - Type: Gene Product:Transporter, Major Facilitator Superfamily (MFS) \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_11530 - mgsA Type: Gene Product:Methylglyoxal synthase (MGS) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_28270 - Type: Gene Product:Transcriptional regulator, MarR family \| Pathway: \| COG: Transcription CD630_28250 - Type: Gene Product:Putative flavodoxin \| Pathway: \| COG: Energy production and conversion CD630_28280 - Type: Gene Product:Putative pyridoxal phosphate-dependenttransferase \| Pathway: \| COG: Amino acid transport and metabolism CD630_33260 - Type: Gene Product:Integrase, lambdoid phage family Tn916-like,CTn6-Orf1 \| Pathway: \| COG: Replication, recombination and repair CD630_11500 - minD Type: Gene Product:Septum site-determining protein MinD (Celldivision inhibitor MinD) \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning CD630_11490 - minC Type: Gene Product:Cell division regulator (septum placement) \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning CD630_02770 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_11470 - Type: Gene Product:Putative permease \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_11520 - mrdB Type: Gene Product:Rod shape-determining protein MrdB \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning CD630_11450 - mreB2 Type: Gene Product:Rod shape-determining protein MreB \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning CD630_28260 - Type: Gene Product:Putative aldolase \| Pathway: \| COG: Energy production and conversion CD630_11430 - Type: Gene Product:Putative Maf-like protein \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning CD630_27040 - Type: Gene Product:Putative permease \| Pathway: \| COG: Function unknown CD630_05103 - Type: Gene Product:Putative conjugative transposon protein Tn5397,CTn3-Orf4 \| Pathway: \| COG: CD630_33270 - Type: Gene Product:Putative conjugative transposon proteinTn916-like, CTn6-Orf2 \| Pathway: \| COG: Function unknown	`NA`	`NA`	0.46	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_17820 - 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_27	1 CD630_16630 - guaD Type: Gene Product:Guanine deaminase (Guanase) (Guanine aminase)(Guanine aminohydrolase) (GAH) \| Pathway: \| COG: Nucleotide transport and metabolism	`NA`	`NA`	1.00	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_26650 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_30940 - Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_207	8 CD630_06750 - Type: Gene Product:Putative acetyltransferase \| Pathway: \| COG: Function unknown CD630_08450 - Type: Gene Product:Putative nuclease \| Pathway: \| COG: Transcription CD630_13430 - glnA Type: Gene Product:Glutamine synthetase \| Pathway: \| COG: Amino acid transport and metabolism CD630_08460 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_21500 - Type: Gene Product:Putative endonuclease/exonuclease/phosphatase \| Pathway: \| COG: Function unknown CD630_24310 - Type: Gene Product:Putative nitrite/sulphite reductase \| Pathway: \| COG: Energy production and conversion CD630_35512 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_06550 - Type: Gene Product:Putative beta-lactamase-like protein \| Pathway: \| COG: Function unknown	`NA`	`NA`	0.65	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_28690 - Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| 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`