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_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_95	30 CD630_30090 - Type: Gene Product:Putative pyridine nucleotide-disulphideoxidoreductase, class I \| Pathway: \| COG: Energy production and conversion CD630_32410 - prdB Type: Gene Product:Proline reductase (selenocysteine) \| Pathway: \| COG: Function unknown CD630_01700 - Type: Gene Product:ABC-type transport system, ATP-binding protein \| Pathway: \| COG: Function unknown CD630_24050 - Type: Gene Product:Transcriptional regulator, MarR family \| Pathway: \| COG: Transcription CD630_07790 - Type: Gene Product:Putative amidohydrolase, M20D peptidase family \| Pathway: \| COG: Amino acid transport and metabolism CD630_07910 - Type: Gene Product:Conserved hypothetical protein, UPF0029 family \| Pathway: \| COG: Function unknown CD630_32380 - Type: Gene Product:Putative component of proline reductaseprdE-like \| Pathway: \| COG: Function unknown CD630_30100 - Type: Gene Product:Putative cytochrome C assembly protein \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_07770 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_24080 - Type: Gene Product:Putative multidrug efflux pump \| Pathway: \| COG: Function unknown CD630_12810 - mnmA Type: Gene Product:tRNA-specific 2-thiouridylase MnmA \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_07040 - Type: Gene Product:Putative metal-dependent phosphohydrolase \| Pathway: \| COG: Function unknown CD630_24060 - Type: Gene Product:Putative lipoprotein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_01710 - rex Type: Gene Product:Transcriptional regulator, Redox-sensingrepressor Rex \| Pathway: \| COG: Transcription CD630_32400 - prdD Type: Gene Product:Proline reductase PrdD \| Pathway: \| COG: Function unknown CD630_07780 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_14930 - Type: Gene Product:Putative 3-methyladenine DNA glycosylase \| Pathway: \| COG: Replication, recombination and repair CD630_24070 - Type: Gene Product:Putative multidrug efflux pump \| Pathway: \| COG: Defense mechanisms CD630_10620 - acpP Type: Gene Product:Acyl carrier protein (ACP) \| Pathway: Lipid metabolism \| COG: Lipid transport and metabolism CD630_07800 - Type: Gene Product:Conserved hypothetical protein, DUF1177 family \| Pathway: \| COG: Function unknown CD630_01690 - Type: Gene Product:Putative drug/sodium antiporter, MATE family \| Pathway: \| COG: Defense mechanisms CD630_16740 - Type: Gene Product:Putative NADPH-dependent FMN reductase \| Pathway: \| COG: Function unknown CD630_30110 - Type: Gene Product:Transcriptional regulator, HxlR family DUF24 \| Pathway: \| COG: Transcription CD630_07030 - Type: Gene Product:Putative peptidase, U32 family \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_32390 - prdE Type: Gene Product:Proline reductase PrdE \| Pathway: \| COG: Function unknown CD630_07050 - Type: Gene Product:Putative hydrolase, NUDIX family \| Pathway: \| COG: Replication, recombination and repair CD630_32360 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_32370 - prdF Type: Gene Product:Proline racemase \| Pathway: \| COG: Amino acid transport and metabolism CD630_31080 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_24730 - rpsT Type: Gene Product:30S ribosomal protein S20 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis	0.00000046	0.72	0.51	Inferelator: 3 Hypergeometric: 3 TF Influences from Inferelator CD630_06700 - Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription CD630_18100 - Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription CD630_24120 - Type: Gene Product:Putative negative regulator of gluconeogenesis \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test 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 CD630_31760 - glnF Type: Gene Product:RNA polymerase sigma-54 factor \| 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_97	29 CD630_33020 - chrA Type: Gene Product:Chromate transport protein ChrA \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_35960 - Type: Gene Product:putative homocysteine S-methyltransferase \| Pathway: \| COG: Amino acid transport and metabolism CD630_35980 - luxS Type: Gene Product:S-ribosylhomocysteine lyase (Autoinducer-2production protein luxS) (AI-2 synthesis protein) \| Pathway: \| COG: Signal transduction mechanisms CD630_13410 - exoA Type: Gene Product:Exodeoxyribonuclease \| Pathway: \| COG: Replication, recombination and repair CD630_00150 - tadA Type: Gene Product:tRNA specific adenosine deaminase \| Pathway: \| COG: Nucleotide transport and metabolism, Translation, ribosomal structure and biogenesis CD630_05220 - Type: Gene Product:Putative c-di-GMP regulatory protein \| Pathway: \| COG: Signal transduction mechanisms CD630_06940 - Type: Gene Product:Transcriptional regulator, TetR family \| Pathway: \| COG: Transcription CD630_21080 - Type: Gene Product:Putative drug/sodium antiporter, MATE family \| Pathway: \| COG: Defense mechanisms CD630_11850 - Type: Gene Product:Putative diguanylate kinase signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_15680 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_32300 - bclA2 Type: Gene Product:Exosporium glycoprotein \| Pathway: \| COG: Function unknown CD630_08280 - Type: Gene Product:Putative oxidative stress glutamate synthase \| Pathway: \| COG: Amino acid transport and metabolism CD630_15340 - ggt Type: Gene Product:Gamma-glutamyltranspeptidase \| Pathway: \| COG: Amino acid transport and metabolism CD630_35970 - Type: Gene Product:Putative S-adenosyl-L-methionine dependentmethionine synthase \| Pathway: \| COG: Function unknown CD630_32320 - CdsB Type: Gene Product:Cysteine desulfidase \| Pathway: \| COG: Function unknown 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_06950 - Type: Gene Product:Putative exported metalloendopeptidase \| Pathway: \| COG: Amino acid transport and metabolism CD630_32310 - hpt Type: Gene Product:Hypoxanthine phosphoribosyltransferase \| Pathway: Purine metabolism \| COG: Nucleotide transport and metabolism CD630_21090 - Type: Gene Product:Putative anion:Na+ symporter \| Pathway: \| COG: Function unknown CD630_05230 - Type: Gene Product:Putative transcriptional regulator \| Pathway: \| COG: Function unknown CD630_08250 - rbr Type: Gene Product:Rubrerythrin \| Pathway: \| COG: Energy production and conversion CD630_28870 - Type: Gene Product:Putative diguanylate kinase signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_07070 - Type: Gene Product:Putative diguanylate kinase signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_25150 - Type: Gene Product:Putative L-aspartate-beta-decarboxylase \| Pathway: \| COG: Amino acid transport and metabolism CD630_22610 - Type: Gene Product:Putative peptidase, M24 family \| Pathway: \| COG: Amino acid transport and metabolism	1.5e-18	`NA`	0.51	Inferelator: 4 Hypergeometric: 0 TF Influences from Inferelator CD630_12390 - Type: Gene Product:Transcriptional regulator, beta-lactams repressorPhage-type \| Pathway: \| COG: Transcription CD630_16930 - Type: Gene Product:Putative dinitrogenase iron-molybdenum cofactor \| Pathway: \| COG: Function unknown CD630_19100 - eutV Type: Gene Product:Two-component response regulator, Ethanolaminespecific \| Pathway: \| COG: Signal transduction mechanisms 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_98	23 CD630_27260 - glyA Type: Gene Product:Serine hydroxymethyltransferase \| Pathway: One-carbon metabolism \| COG: Amino acid transport and metabolism CD630_10030 - fumA Type: Gene Product:Fumarate hydratase class I, subunit A \| Pathway: \| COG: Energy production and conversion CD630_22080 - Type: Gene Product:Transcriptional regulator, MarR family \| Pathway: \| COG: Transcription CD630_17500 - Type: Gene Product:Putative CoA enzyme activase \| Pathway: \| COG: Lipid transport and metabolism CD630_10050 - Type: Gene Product:Putative NAD-dependent malic enzyme \| Pathway: \| COG: Energy production and conversion CD630_06670 - cdd4 Type: Gene Product:ABC-type transport system,lantibiotic/multidrug-family ATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_06650 - cdd2 Type: Gene Product:ABC-type transport system,lantibiotic/multidrug-family permease \| Pathway: \| COG: Function unknown CD630_06690 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_17490 - Type: Gene Product:Putative 2-hydroxyacyl-CoA dehydratase \| Pathway: \| COG: Amino acid transport and metabolism CD630_23080 - Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription CD630_09770 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_09750 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_27270 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_09870 - Type: Gene Product:Putative phosphatase/hydrolase \| Pathway: \| COG: Replication, recombination and repair CD630_10040 - fumB Type: Gene Product:Fumarate hydratase class I, subunit B \| Pathway: \| COG: Energy production and conversion CD630_06660 - cdd3 Type: Gene Product:ABC-type transport system,lantibiotic/multidrug-family permease \| Pathway: \| COG: Function unknown CD630_06680 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_27280 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_23070 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_09880 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_09760 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_13920 - Type: Gene Product:Putative endoribonuclease \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_22070 - Type: Gene Product:Putative flavodoxin \| Pathway: \| COG: Function unknown	0.00019	0	0.50	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_99	26 CD630_05940 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_10230 - Type: Gene Product:Putative transcriptional regulator, HTH \| Pathway: \| COG: Transcription CD630_23850 - Type: Gene Product:Putative diguanylate cyclase signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_17520 - Type: Gene Product:Transcriptional regulator, TetR family \| Pathway: \| COG: Transcription CD630_23860 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_17560 - def1 Type: Gene Product:Peptide deformylase 1 (PDF 1) (Polypeptidedeformylase 1) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_17570 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_17540 - Type: Gene Product:ABC-type transport system, multidrug-familypermease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_25190 - Type: Gene Product:Integrase \| Pathway: \| COG: Replication, recombination and repair CD630_10240 - potA Type: Gene Product:ABC-type transport system, spermidine/putrescineATP-binding protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_22280 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_23770 - Type: Gene Product:Putative hydrolase, NUDIX family \| Pathway: \| COG: Replication, recombination and repair CD630_23840 - Type: Gene Product:Putative diguanylate cyclase signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_10260 - potC Type: Gene Product:ABC-type transport system, spermidine/putrescinepermease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_05950 - Type: Gene Product:Putative nuclease, ParB-like \| Pathway: \| COG: Transcription CD630_17530 - Type: Gene Product:ABC-type transport system, multidrug-familyATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_28420 - Type: Gene Product:Nitrilase (carbon-nitrogen hydrolase) \| Pathway: \| COG: Function unknown CD630_23830 - Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription CD630_23780 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_17550 - Type: Gene Product:ABC-type transport system, multidrug-familypermease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_17551 - Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription CD630_22270 - Type: Gene Product:Putative radical SAM superfamily lipoprotein \| Pathway: \| COG: Energy production and conversion CD630_25180 - cwp29 Type: Gene Product:Cell surface protein \| Pathway: \| COG: Function unknown CD630_10250 - potB Type: Gene Product:ABC-type transport system, spermidine/putrescinepermease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_10270 - potD Type: Gene Product:ABC-type transport system, spermidine/putrescinesolute-binding protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_17580 - Type: Gene Product:Putative radical SAM superfamily protein \| Pathway: \| COG: Replication, recombination and repair	0.01	0.56	0.64	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator 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`