Organism : Clostridium acetobutylicum | Module List :
Sporulation protein IVFB related protein, predicted metallopeptidase (NCBI ptt file)
Functional Annotations (4)
|Zn-dependent proteases||cog/ cog|
|metalloendopeptidase activity||go/ molecular_function|
|zinc ion binding||go/ molecular_function|
Regulation information for CAC1253(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|
Functional Enrichment for CAC1253
Module neighborhood information for CAC1253
|Gene||Common Name||Description||Module membership|
|CAC0262||CAC0262||Tryptophan-rich possible sensory protein, TSPO homolog (NCBI ptt file)||95, 279|
|CAC0283||CAC0283||Molybdopterin biosynthesis protein (NCBI ptt file)||95, 290|
|CAC0344||CAC0344||Hypothetical protein (NCBI ptt file)||39, 95|
|CAC0455||CAC0455||Hypothetical protein (NCBI ptt file)||95, 177|
|CAC0486||CAC0486||Hypothetical protein (NCBI ptt file)||73, 367|
|CAC0546||CAC0546||Uncharacterized membrane protein, homolog of Methanobacterium (2621593) (NCBI ptt file)||95, 304|
|CAC0642||CAC0642||Conserved domain seen in the bacterial SpoT (NCBI ptt file)||73, 367|
|CAC0681||nrgB||Nitrogen regulatory protein PII, gene nrgB (NCBI ptt file)||235, 367|
|CAC0703||CAC0703||Sugar ABC-transporter, ATP-ase component (NCBI ptt file)||95, 137|
|CAC0704||CAC0704||Sugar ABC transporter, permease protein (NCBI ptt file)||95, 174|
|CAC0803||CAC0803||Hypothetical protein (NCBI ptt file)||328, 367|
|CAC0808||hybG||Hydrogenase expression factor (hybG) (NCBI ptt file)||95, 290|
|CAC0809||hypE||Hydrogenase formation factor (hypE) (NCBI ptt file)||95, 290|
|CAC0810||hypF||Hydrogenase maturation factor (hypF) (NCBI ptt file)||95, 300|
|CAC0841||CAC0841||Predicted transcriptional regulator (NCBI ptt file)||15, 367|
|CAC1020||CAC1020||Hypothetical protein (NCBI ptt file)||80, 367|
|CAC1055||CAC1055||Hypothetical protein (NCBI ptt file)||38, 367|
|CAC1253||CAC1253||Sporulation protein IVFB related protein, predicted metallopeptidase (NCBI ptt file)||95, 367|
|CAC1326||CAC1326||Uncharacterized protein homolog T.maritima (4980675) (NCBI ptt file)||39, 95|
|CAC1402||CAC1402||Unchracterized conserved protein, similar to IcaC of Staphylococcus; YHJR B.subtilis family (NCBI ptt file)||39, 95|
|CAC1430||CAC1430||Transcriptional regulators of sugar metabolism (deoR family) (NCBI ptt file)||95, 142|
|CAC1432||CAC1432||Undecaprenyl pyrophosphate synthase related enzyme (NCBI ptt file)||95, 179|
|CAC1486||CAC1486||Uncharacterized protein, ortholog of YKUS B.subtilis (NCBI ptt file)||118, 367|
|CAC1509||CAC1509||Specialized sigma subunit of RNA polymerase (NCBI ptt file)||305, 367|
|CAC1567||CAC1567||Hypothetical protein (NCBI ptt file)||95, 367|
|CAC2363||CAC2363||Uncharacterized protein, YtxC B.subtilis homolog (NCBI ptt file)||95, 279|
|CAC2465||CAC2465||Uncharacterized conserved protein (NCBI ptt file)||73, 367|
|CAC2488||CAC2488||Uncharacterized conserved protein, YTFE family (NCBI ptt file)||285, 367|
|CAC2802||CAC2802||Predicted phosphoglycerol transferase (alkaline phosphatase superfamily), YFNI B.subtilis (NCBI ptt file)||73, 367|
|CAC2876||CAC2876||Deoxycytidylate deaminase (NCBI ptt file)||15, 367|
|CAC3016||CAC3016||Uncharacterized conserved membrane protein (NCBI ptt file)||95, 118|
|CAC3019||CAC3019||Sensory transduction protein with GGDEF and EAL domains (NCBI ptt file)||73, 367|
|CAC3176||ilvN||Acetolactate synthase, small subunit (NCBI ptt file)||29, 367|
|CAC3186||CAC3186||Hypothetical protein (NCBI ptt file)||95, 273|
|CAC3205||spoIIE||Stage II sporulation protein E, serine phosphatase family (NCBI ptt file)||42, 367|
|CAC3393||CAC3393||Hypothetical protein (NCBI ptt file)||80, 367|
|CAC3727||CAC3727||Uncharacterized protein, YYAC B.subtilis homolog (NCBI ptt file)||95, 367|
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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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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Module Members Tab
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;
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