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 71 - 80 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_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_108	11 CD630_05240 - Type: Gene Product:Putative peptidase, M20 family \| Pathway: \| COG: Amino acid transport and metabolism CD630_17151 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_08660 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_18990 - Type: Gene Product:Putative dCMP deaminase \| Pathway: \| COG: Nucleotide transport and metabolism CD630_15960 - map2 Type: Gene Product:Methionine aminopeptidase Map2 (MAP) (PeptidaseM) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_08990 - dinB Type: Gene Product:DNA polymerase IV (Pol IV) \| Pathway: \| COG: Replication, recombination and repair CD630_14680 - Type: Gene Product:Putative iron-sulfur protein \| Pathway: \| COG: Energy production and conversion CD630_21241 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_17770 - Type: Gene Product:Putative arsenate reductase \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_06550 - Type: Gene Product:Putative beta-lactamase-like protein \| Pathway: \| COG: Function unknown CD630_23040 - Type: Gene Product:Transcriptional regulator, beta-lactams repressorPhage-type \| Pathway: \| COG: Transcription	`NA`	`NA`	0.51	Inferelator: 3 Hypergeometric: 0 TF Influences from Inferelator 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_26650 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_28	16 CD630_00780 - rplV Type: Gene Product:50S ribosomal protein L22 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00870 - rplR Type: Gene Product:50S ribosomal protein L18 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00730 - rplC Type: Gene Product:50S ribosomal protein L3 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00790 - rpsC Type: Gene Product:30S ribosomal protein S3 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00890 - rplO Type: Gene Product:50S ribosomal protein L15 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00950 - rpsM Type: Gene Product:30S ribosomal protein S13 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00940 - infA Type: Gene Product:Translation initiation factor IF-1 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00740 - rplD Type: Gene Product:50S ribosomal protein L4 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00900 - prlA Type: Gene Product:Preprotein translocase SecY subunit \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_01040 - rplM Type: Gene Product:50S ribosomal protein L13 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00770 - rpsS Type: Gene Product:30S ribosomal protein S19 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00700 - fusA Type: Gene Product:Elongation factor G (EF-G) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00920 - map1 Type: Gene Product:Methionine aminopeptidase Map1 (MAP) (PeptidaseM) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00910 - adk Type: Gene Product:Adenylate kinase \| Pathway: Purine metabolism \| COG: Nucleotide transport and metabolism CD630_00820 - rplN Type: Gene Product:50S ribosomal protein L14 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00930 - Type: Gene Product:Ribosomal protein L14E/L6E/L27E-like \| Pathway: \| COG: Function unknown	`NA`	`NA`	0.12	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_02760 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_16860 - Type: Gene Product:Transcriptional regulator, repressor-like \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_44	21 CD630_16360 - terD Type: Gene Product:Tellurium resistance protein \| Pathway: \| COG: Signal transduction mechanisms CD630_25900 - dapF Type: Gene Product:Diaminopimelate epimerase (DAP epimerase) \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_16370 - Type: Gene Product:Putative calcium-transporting ATPase \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_25780 - Type: Gene Product:Putative serine/threonine-protein kinase andphosphatase \| Pathway: \| COG: Signal transduction mechanisms CD630_16350 - terD Type: Gene Product:Tellurium resistance protein \| Pathway: \| COG: Signal transduction mechanisms CD630_25790 - Type: Gene Product:Putative phosphatase, 2C family \| Pathway: \| COG: Signal transduction mechanisms CD630_25810 - rsmB Type: Gene Product:Ribosomal RNA small subunit methyltransferase B(rRNA (cytosine-C(5)-)-methyltransferase) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_16400 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_25830 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_16410 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_25740 - thiN Type: Gene Product:Thiamine pyrophosphokinase (TPK) (Thiaminediphospho kinase) \| Pathway: \| COG: Coenzyme transport and metabolism CD630_13580 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_16430 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_25770 - fabG Type: Gene Product:3-oxoacyl-[acyl-carrier-protein] reductase(3-ketoacyl- acyl carrier protein reductase) \| Pathway: \| COG: Function unknown CD630_16380 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_16420 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_25860 - priA Type: Gene Product:Primosomal protein N' (ATP-dependent helicasepriA) (Replication factor Y) \| Pathway: \| COG: Replication, recombination and repair CD630_16390 - Type: Gene Product:Putative tellurite associated resistance protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_16330 - Type: Gene Product:Putative serine protease \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_13570 - Type: Gene Product:Putative peptidyl-prolyl isomerase \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_25871 - rpoZ Type: Gene Product:DNA-directed RNA polymerase subunit omega (RNAPomega subunit) (Transcriptase subunit omega) (RNApolymerase omega subunit) \| Pathway: \| COG: Transcription	`NA`	`NA`	0.48	Inferelator: 4 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_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_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_184	21 CD630_02480 - fliF Type: Gene Product:Flagellar M-ring protein FliF \| Pathway: \| COG: Cell motility CD630_02620 - flhB Type: Gene Product:Bifunctional flagellar biosynthesis proteinFliR/FlhB \| Pathway: \| COG: Cell motility CD630_02630 - flhA Type: Gene Product:Flagellar biosynthesis protein FlhA \| Pathway: \| COG: Cell motility CD630_02490 - fliG Type: Gene Product:Flagellar motor switch protein FliG \| Pathway: \| COG: Cell motility CD630_02640 - flhF Type: Gene Product:Flagellar biosynthesis regulator FlhF(Flagella-associated GTP-binding protein) \| Pathway: \| COG: Cell motility CD630_02510 - fliI Type: Gene Product:ATP synthase subunit beta FliI \| Pathway: \| COG: Cell motility, Intracellular trafficking, secretion, and vesicular transport CD630_02650 - flhG Type: Gene Product:Flagellar number regulator FlhG \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning CD630_02470 - fliE Type: Gene Product:Flagellar hook-basal body complex protein FliE \| Pathway: \| COG: Cell motility CD630_02600 - fliP Type: Gene Product:Flagellar biosynthesis protein FliP \| Pathway: \| COG: Cell motility CD630_02551 - FlbD Type: Gene Product:Flagellar protein FlbD \| Pathway: \| COG: Cell motility CD630_02530 - fliK Type: Gene Product:Flagellar hook-length control protein FliK \| Pathway: \| COG: Cell motility CD630_02460 - flgC Type: Gene Product:Flagellar basal-body rod protein FlgC \| Pathway: \| COG: Cell motility CD630_02520 - fliJ Type: Gene Product:Flagellar protein FliJ \| Pathway: \| COG: Cell motility CD630_02570 - motB Type: Gene Product:Flagellar motor rotation protein MotB (Chemotaxisprotein MotB) \| Pathway: \| COG: Cell motility CD630_02670 - Type: Gene Product:Putative flagellar protein \| Pathway: \| COG: CD630_02560 - motA Type: Gene Product:Flagellar motor rotation protein MotA \| Pathway: \| COG: Cell motility CD630_02540 - flgD Type: Gene Product:Basal-body rod modification protein FlgD \| Pathway: \| COG: Cell motility CD630_02450 - flgB Type: Gene Product:Flagellar basal-body rod protein FlgB \| Pathway: \| COG: Cell motility CD630_02580 - fliL Type: Gene Product:Flagellar basal body-associated protein FliL \| Pathway: \| COG: Cell motility CD630_02660 - sigD Type: Gene Product:RNA polymerase sigma-28 factor for flagellaroperon \| Pathway: \| COG: Transcription CD630_02610 - fliQ Type: Gene Product:Flagellar biosynthetic protein FliQ \| Pathway: \| COG: Cell motility	`NA`	`NA`	0.37	Inferelator: 2 Hypergeometric: 1 TF Influences from Inferelator CD630_02660 - sigD Type: Gene Product:RNA polymerase sigma-28 factor for flagellaroperon \| Pathway: \| COG: Transcription CD630_22140 - SinR Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_02660 - sigD Type: Gene Product:RNA polymerase sigma-28 factor for flagellaroperon \| Pathway: \| COG: Transcription
Module_280	9 CD630_31470 - Type: Gene Product:Putative DNA-methyltransferase \| Pathway: \| COG: Replication, recombination and repair CD630_21341 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_13940 - Type: Gene Product:Putative NAD(P)-binding oxidoreductase,GFO/IDH/MOCA family \| Pathway: \| COG: Function unknown CD630_32330 - Type: Gene Product:Putative sigma-54 interacting protein \| Pathway: \| COG: Transcription CD630_17800 - Type: Gene Product:Putative methylase \| Pathway: \| COG: Replication, recombination and repair CD630_05850 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription CD630_21820 - Type: Gene Product:Fragment of conserved hypothetical protein(C-terminal region) \| Pathway: \| COG: Function unknown CD630_34500 - Type: Gene Product:Putative oxidoreductase with NAD(P)-bindingRossmann-fold domain \| Pathway: \| COG: Function unknown CD630_17780 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown	`NA`	`NA`	0.53	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_16930 - Type: Gene Product:Putative dinitrogenase iron-molybdenum cofactor \| Pathway: \| COG: Function unknown 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_156	5 CD630_25010 - Type: Gene Product:Putative hydrolase, HAD superfamily, IIBsubfamily \| Pathway: \| COG: Function unknown CD630_15980 - Type: Gene Product:Putative excinuclease ABC-like \| Pathway: \| COG: Replication, recombination and repair CD630_23910 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_05320 - Type: Gene Product:Putative transcriptional regulator \| Pathway: \| COG: Transcription CD630_23150 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown	`NA`	`NA`	0.54	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_23160 - 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_312	5 CD630_18781 - Type: Gene Product:Fragment of conserved hypothetical protein(N-terminal region) \| Pathway: \| COG: Replication, recombination and repair CD630_13750 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_21840 - Type: Gene Product:Putative N-acetylmuramoyl-L-alanine amidase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_18441 - Type: Gene Product:Fragment of putative methyltransferase(N-terminal region) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_36130 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown	`NA`	`NA`	0.52	Inferelator: 3 Hypergeometric: 0 TF Influences from Inferelator CD630_15840 - Type: Gene Product:Transcriptional regulator, repressor ROK family \| Pathway: \| COG: Carbohydrate transport and metabolism, Transcription 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_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_45	5 CD630_29960 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_16660 - Type: Gene Product:Putative membrane glycerophosphoryl diesterphosphodiesterase \| Pathway: \| COG: Energy production and conversion CD630_21650 - Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription CD630_06040 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_01590 - Type: Gene Product:Putative enzyme, glyoxalase family \| Pathway: \| COG: Amino acid transport and metabolism	`NA`	`NA`	0.59	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_13790 - Type: Gene Product:Transcriptional regulator, Phage-type \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`