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 401 - 406 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_100	21 CD630_20400 - Type: Gene Product:Transcriptional regulator, MerR family \| Pathway: \| COG: Transcription CD630_16632 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_05160 - Type: Gene Product:Transcription antiterminator \| Pathway: \| COG: Signal transduction mechanisms CD630_02731 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_06250 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_20051 - Type: Gene Product:Fragment of conserved hypothetical protein(N-terminal region) \| Pathway: \| COG: Transcription CD630_22290 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_06240 - Type: Gene Product:Putative transcriptional regulator, activatorMor \| Pathway: \| COG: Transcription CD630_17870 - Type: Gene Product:Transcriptional regulator, MerR family \| Pathway: \| COG: Transcription CD630_11031 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn4-Orf20 \| Pathway: \| COG: CD630_05150 - Type: Gene Product:D-alanyl-D-alanine carboxypeptidase, S11peptidase family \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_09060 - Type: Gene Product:Putative phage DNA-binding protein \| Pathway: \| COG: CD630_02440 - Type: Gene Product:Putative CDP-glycerol:Poly(glycerophosphate)glycerophosphotransferase \| Pathway: \| COG: Function unknown CD630_18800 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_26280 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_16731 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_14181 - Type: Gene Product:Fragment of putative phage protein (Part 3) \| Pathway: \| COG: Replication, recombination and repair, Replication, recombination and repair CD630_17590 - Type: Gene Product:Putative SAM-dependent methyltransferase \| Pathway: \| COG: Function unknown CD630_05621 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_01340 - Type: Gene Product:Transcription antiterminator, PTS operonregulator \| Pathway: \| COG: Transcription CD630_02010 - Type: Gene Product:Putative chromate transporter \| Pathway: \| COG: Inorganic ion transport and metabolism	7.7	`NA`	0.60	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_05160 - Type: Gene Product:Transcription antiterminator \| Pathway: \| COG: Signal transduction mechanisms CD630_27320 - Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_220	16 CD630_27210 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_22200 - Type: Gene Product:Putative cyclic nucleotides-binding protein \| Pathway: \| COG: Signal transduction mechanisms CD630_32610 - pstB Type: Gene Product:ABC-type transport system, phosphate-specificATP-binding \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_31650 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Replication, recombination and repair CD630_31660 - Type: Gene Product:Transcriptional regulator, hxlR family \| Pathway: \| COG: Transcription CD630_31670 - Type: Gene Product:Putative phosphatidylethanolamine-bindingregulatory protein \| Pathway: \| COG: Function unknown CD630_32630 - pstC Type: Gene Product:ABC-type transport system, phosphate-specificpermease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_32620 - pstA Type: Gene Product:ABC-type transport system, phosphate-specificpermease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_20530 - lysA Type: Gene Product:Diaminopimelate decarboxylase \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_32600 - phoU Type: Gene Product:Phosphate uptake regulator, PhoU \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_27220 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_20540 - lysC Type: Gene Product:Aspartokinase \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism	7.8	2.2	0.36	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_22200 - Type: Gene Product:Putative cyclic nucleotides-binding protein \| Pathway: \| COG: Signal transduction mechanisms CD630_27220 - 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_132	12 CD630_29960 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_20260 - Type: Gene Product:Putative acetyltransferase \| Pathway: \| COG: Function unknown CD630_36210 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_20270 - Type: Gene Product:N-carbamoyl-L-amino acid hydrolase \| Pathway: \| COG: Amino acid transport and metabolism CD630_25410 - Type: Gene Product:Sodium:glutamate/aspartate symporter family \| Pathway: \| COG: Function unknown CD630_02791 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_36200 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_20280 - Type: Gene Product:Putative aspartate racemase RacX \| Pathway: \| COG: Amino acid transport and metabolism CD630_36690 - Type: Gene Product:Putative lipoprotein \| Pathway: \| COG: Function unknown CD630_00210 - pycA Type: Gene Product:Pyruvate carboxylase \| Pathway: \| COG: Energy production and conversion CD630_16660 - Type: Gene Product:Putative membrane glycerophosphoryl diesterphosphodiesterase \| Pathway: \| COG: Energy production and conversion CD630_25170 - Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription	8.3	`NA`	0.69	Inferelator: 3 Hypergeometric: 0 TF Influences from Inferelator CD630_10090 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription CD630_20600 - Type: Gene Product:Putative lipid kinase \| Pathway: \| COG: Lipid transport and metabolism 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_89	27 CD630_26550 - murF Type: Gene Product:UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase (UDP-MurNAc-pentapeptide synthetase)(D-alanyl-D-alanine-adding enzyme) \| Pathway: Cell wall biogenesis \| COG: Cell wall/membrane/envelope biogenesis CD630_34380 - cobU Type: Gene Product:Bifunctional adenosylcobalamin biosynthesisprotein CobU [Adenosylcobinamide kinase;Adenosylcobinamide-phosphate guanylyltransferase] \| Pathway: \| COG: Coenzyme transport and metabolism CD630_26470 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_18150 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_26490 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_35880 - carB1 Type: Gene Product:Carbamoyl-phosphate synthase large chain 1 \| Pathway: Amino-acid biosynthesis \| COG: Nucleotide transport and metabolism CD630_18170 - Type: Gene Product:Putative acyltransferase \| Pathway: \| COG: Lipid transport and metabolism CD630_35400 - metG Type: Gene Product:Methionyl-tRNA synthetase (Methionine--tRNAligase) (MetRS) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_34370 - cobS Type: Gene Product:Cobalamin synthase CobS (Cobalamin-5-phosphatesynthase) \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_26520 - spoVE Type: Gene Product:Cell division/stage V sporulation protein \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning CD630_35390 - Type: Gene Product:Putative deoxyribonuclease \| Pathway: \| COG: Replication, recombination and repair CD630_18140 - Type: Gene Product:Putative phosphoglycerate mutase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_35910 - carA Type: Gene Product:Carbamoyl-phosphate synthase small chain \| Pathway: Amino-acid biosynthesis \| COG: Nucleotide transport and metabolism CD630_36250 - Type: Gene Product:Putative signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_26500 - Type: Gene Product:Putative cell division protein Fts-Q type \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_18160 - cmk Type: Gene Product:Cytidylate kinase (CK) (Cytidine monophosphatekinase) (CMP kinase) \| Pathway: \| COG: Nucleotide transport and metabolism CD630_26540 - mraY Type: Gene Product:Phospho-N-acetylmuramoyl-pentapeptide-transferase(UDP- MurNAc-pentapeptide phosphotransferase) \| Pathway: Cell wall biogenesis \| COG: Cell wall/membrane/envelope biogenesis CD630_35890 - carA Type: Gene Product:Carbamoyl-phosphate synthase small chain \| Pathway: Amino-acid biosynthesis \| COG: Nucleotide transport and metabolism CD630_34390 - cobT Type: Gene Product:Nicotinate-nucleotide--dimethylbenzimidazolephosphoribosyltransferase (NN:DBI PRT)(N(1)-alpha-phosphoribosyltransferase) \| Pathway: Nucleoside biosynthesis \| COG: Coenzyme transport and metabolism CD630_26480 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_24800 - Type: Gene Product:Putative hydrolase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_18180 - ispH Type: Gene Product:4-hydroxy-3-methylbut-2-enyl diphosphatereductase \| Pathway: Isoprenoid biosynthesis \| COG: Lipid transport and metabolism CD630_34360 - cobC Type: Gene Product:Cobalamin biosynthesis phosphoglycerate mutaseCobC \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_35920 - pyrF Type: Gene Product:Orotidine 5'-phosphate decarboxylase (OMPdecarboxylase) (OMPDCase) (OMPdecase) \| Pathway: Pyrimidine metabolism \| COG: Nucleotide transport and metabolism CD630_26530 - murD Type: Gene Product:UDP-N-acetylmuramoylalanine--D-glutamate ligase(UDP-N- acetylmuramoyl-L-alanyl-D-glutamate synthetase)(D-glutamic acid- adding enzyme) \| Pathway: Cell wall biogenesis \| COG: Cell wall/membrane/envelope biogenesis CD630_26510 - murG Type: Gene Product:UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosaminetransferase \| Pathway: Cell wall biogenesis \| COG: Cell wall/membrane/envelope biogenesis CD630_35900 - carB2 Type: Gene Product:Carbamoyl-phosphate synthase large chain 2 \| Pathway: Amino-acid biosynthesis \| COG: Nucleotide transport and metabolism	8.7	`NA`	0.47	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_4	13 CD630_34180 - sirC Type: Gene Product:Precorrin-2 dehydrogenase \| Pathway: Porphyrin-containing compound metabolism \| COG: Coenzyme transport and metabolism CD630_34320 - cobD Type: Gene Product:Threonine-phosphate decarboxylase(L-threonine-O-3-phosphate decarboxylase), CobD/CbiBfamily \| Pathway: \| COG: Amino acid transport and metabolism CD630_34190 - hemB Type: Gene Product:Delta-aminolevulinic acid dehydratase(porphobilinogen synthase) \| Pathway: \| COG: Coenzyme transport and metabolism CD630_11800 - fabK Type: Gene Product:Enoyl-(Acyl-carrier-protein) reductase II \| Pathway: \| COG: Lipid transport and metabolism CD630_34270 - cbiT Type: Gene Product:Cobalt-precorrin-6Y C(15)-methyltransferase \| Pathway: \| COG: Coenzyme transport and metabolism CD630_34290 - cbiD Type: Gene Product:Cobalt-precorrin-6A synthase [deacetylating] \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_34210 - hemC Type: Gene Product:Porphobilinogen deaminase (PBG)(Hydroxymethylbilane synthase) (HMBS) (Pre-uroporphyrinogensynthase) \| Pathway: Porphyrin-containing compound metabolism \| COG: Coenzyme transport and metabolism CD630_34330 - cbiB Type: Gene Product:Cobalamin biosynthesis protein CbiB, CobD/CbiBfamily \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_34200 - cobA + hemD Type: Gene Product:Bifunctional uroporphyrinogen-IIImethyltransferase/uroporphyrinogen-III synthase \| Pathway: \| COG: Coenzyme transport and metabolism CD630_34310 - Type: Gene Product:Putative cobalamin biosynthesis L-threoninePduX-like kinase \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_11241 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: 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_11790 - fabH Type: Gene Product:3-oxoacyl-[acyl-carrier-protein] synthase 3 \| Pathway: Lipid metabolism \| COG: Lipid transport and metabolism	8.9	`NA`	0.41	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_10090 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription CD630_11770 - fapR Type: Gene Product:Transcriptional regulator, DeoR family (Fattyacid and phospholipid biosynthesis regulator) \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_229	21 CD630_25120 - Type: Gene Product:PTS system, glucose-like IIA component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_31380 - bglG Type: Gene Product:Transcription antiterminator, PTS operonregulator \| Pathway: \| COG: Transcription CD630_25080 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_01360 - Type: Gene Product:PTS system, lactose/cellobiose-family IIBcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_25110 - Type: Gene Product:Transcription antiterminator, PTS operonregulator \| Pathway: \| COG: Transcription CD630_01370 - Type: Gene Product:PTS system, lactose/cellobiose-family IICcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_01380 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_09241 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_15140 - panG Type: Gene Product:Putative ketopantoate reductase \| Pathway: \| COG: Coenzyme transport and metabolism CD630_25090 - Type: Gene Product:Putative glycoside hydrolase, family 4 \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_01410 - cutC Type: Gene Product:Copper homeostasis protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_15130 - panB Type: Gene Product:Ketopantoate hydroxymethyltransferase \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_01390 - Type: Gene Product:N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase \| Pathway: \| COG: Amino acid transport and metabolism CD630_25070 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_15120 - panC Type: Gene Product:Pantothenate synthetase \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_31370 - bglF Type: Gene Product:PTS system, beta-glucoside-specific IIABCcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_01350 - Type: Gene Product:PTS system, lactose/cellobiose-family IIAcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_25100 - Type: Gene Product:PTS system, glucose-like IIBC component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_31360 - bglA Type: Gene Product:6-phospho-beta-glucosidase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_t0860 - tRNA-Glu Type: Gene Product: \| Pathway: \| COG: CD630_01400 - Type: Gene Product:Putative peptidase \| Pathway: \| COG: Amino acid transport and metabolism	9.7	`NA`	0.47	Inferelator: 2 Hypergeometric: 1 TF Influences from Inferelator CD630_10090 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription CD630_25080 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_12750 - codY Type: Gene Product:Transcriptional regulator, GTP-sensingpleiotropic repressor \| Pathway: \| COG: Transcription