Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC2555(Mouseover regulator name to see its description)
Motif information (de novo identified motifs for modules)
There are 4 motifs predicted.
|Motif Id||e-value||Consensus||Motif Logo|
Module neighborhood information for CAC2555
|Gene||Common Name||Description||Module membership|
|CAC0135||CAC0135||Hypothetical protein, CF-23 family (NCBI ptt file)||13, 247|
|CAC0248||CAC0248||Transposon related protein (NCBI ptt file)||13, 117|
|CAC0325||CAC0325||Uncharacterized membrane protein, homolog of YtaF B.subtilis (NCBI ptt file)||13, 117|
|CAC0450||CAC0450||Response regulator (CheY-like and HTH domains) (NCBI ptt file)||13, 66|
|CAC0451||CAC0451||Sensory transduction histidine kinase (HAMP, HisKA, HATPase domains) (NCBI ptt file)||13, 140|
|CAC0569||sacT||SACPA operon antiterminator (sacT) (NCBI ptt file)||149, 277|
|CAC0589||birA||Biotin-(acetyl-CoA carboxylase)ligase (NCBI ptt file)||13, 140|
|CAC0647||CAC0647||Predicted membrane protein (NCBI ptt file)||149, 344|
|CAC0648||CAC0648||Molecular chaperone, DnaJ family (contain C-term. Zn finger domain) (NCBI ptt file)||149, 346|
|CAC0676||pssA||Phosphatidylserine synthase (NCBI ptt file)||149, 282|
|CAC0778||CAC0778||ATP-dependent RNA helicase, superfamily II (NCBI ptt file)||13, 66|
|CAC0820||CAC0820||Conserved protein, ortholog YwqG B.subtilis (NCBI ptt file)||13, 66|
|CAC1012||CAC1012||Uncharacterized membrane protein, homolog of YNGA/YWCD B.suntilis (NCBI ptt file)||13, 69|
|CAC1042||CAC1042||Predicted membrane protein (NCBI ptt file)||149, 296|
|CAC1333||CAC1333||AraC-type sugar metabolism regulator (NCBI ptt file)||149, 252|
|CAC1371||CAC1371||Possible kinase, diverged (NCBI ptt file)||13, 55|
|CAC1381||cbiJ/cobK||precorrin-6x reductase (NCBI ptt file)||13, 55|
|CAC1500||CAC1500||Predicted membrane protein (NCBI ptt file)||13, 351|
|CAC1506||phoP||Response regulator (CheY-like receiver domain and a HTH) (NCBI ptt file)||140, 149|
|CAC1569||CAC1569||Transcriptional regulators, MarR/EmrR family (NCBI ptt file)||149, 252|
|CAC1612||CAC1612||Probable cation efflux pump, multidrug resistance protein (FS) (NCBI ptt file)||76, 149|
|CAC2023||CAC2023||Membrane protein, related to copy number protein COP from Clostridium perfringens plasmid pIP404 (GI:116928) (NCBI ptt file)||60, 149|
|CAC2258||CAC2258||Hypothetical protein (NCBI ptt file)||149, 252|
|CAC2277||secF||Preprotein translocase subunit SecF (NCBI ptt file)||8, 149|
|CAC2348||CAC2348||Glycosyltransferase (NCBI ptt file)||13, 312|
|CAC2349||CAC2349||Hypothetical protein (NCBI ptt file)||13, 100|
|CAC2430||greA||Transcription elongation factor, greA (NCBI ptt file)||149, 252|
|CAC2453||CAC2453||CBS domain containing protein (NCBI ptt file)||13, 346|
|CAC2478||CAC2478||Predicted conserved membrane protein, possible homolog of CAAX-like membrane endopeptidase (NCBI ptt file)||13, 149|
|CAC2515||CAC2515||Hypothetical protein (NCBI ptt file)||149, 341|
|CAC2554||CAC2554||Hypothetical protein (NCBI ptt file)||13, 346|
|CAC2555||CAC2555||Hypothetical protein (NCBI ptt file)||13, 149|
|CAC2851||CAC2851||GntR/FadR-family transcriptional regulator fused to conserved membrane protein (YHCF B.subtilis homolog) (NCBI ptt file)||60, 149|
|CAC2852||comFC||Predicted amidophosphoribosyltransferase, ComFC B.suntilis ortholog (NCBI ptt file)||76, 149|
|CAC2853||CAC2853||Hypothetical protein (NCBI ptt file)||25, 149|
|CAC2907||CAC2907||Glycosyltransferase (NCBI ptt file)||13, 117|
|CAC2940||CAC2940||Membrane-associated sensory histidine kinase-like ATPase (NCBI ptt file)||149, 252|
|CAC3091||CAC3091||Fumarate hydratase, subunit A (N-terminal domain of FumA E.coli) class I (NCBI ptt file)||3, 13|
|CAC3193||CAC3193||Hypothetical protein (NCBI ptt file)||130, 149|
|CAC3240||CAC3240||Predicted membrane protein (NCBI ptt file)||13, 150|
|CAC3265||CAC3265||Predicted membrane protein (NCBI ptt file)||13, 99|
|CAC3587||CAC3587||DNA replication protein DnaD (NCBI ptt file)||13, 287|
|CAC3596||pgsA||Phosphatidylglycerophosphate synthase (NCBI ptt file)||13, 99|
|CAC3692||CAC3692||Hypothetical protein (NCBI ptt file)||13, 196|
Gene Page Help
If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.
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Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.
If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.
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Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.
Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.
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Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.
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CircVisOur circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
- 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
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