Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC3245(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 CAC3245
Module neighborhood information for CAC3245
|Gene||Common Name||Description||Module membership|
|CAC0601||CAC0601||Unchracterized membrane protein, possible permease (NCBI ptt file)||263, 330|
|CAC0609||CAC0609||Cyclic beta 1-2 glucan synthetase (NCBI ptt file)||118, 188|
|CAC0686||CAC0686||Spore cortex-lytic enzyme prepeptide; peptodoglycan-binding domain (NCBI ptt file)||118, 341|
|CAC0769||CAC0769||Uncharacterized conserved protein (NCBI ptt file)||118, 314|
|CAC0857||CAC0857||Glucan phosphorylase (NCBI ptt file)||80, 330|
|CAC0868||CAC0868||Predicted membrane protein (NCBI ptt file)||118, 304|
|CAC1093||CAC1093||Hypothetical secreted protein (NCBI ptt file)||39, 330|
|CAC1252||CAC1252||Possible membrane metalloendopeptidases (NCBI ptt file)||263, 330|
|CAC1276||SpoIIP||Stage II sporulation protein P (NCBI ptt file)||39, 330|
|CAC1298||CAC1298||Uncharacterized protein, related to B.subtilis spore coat protein COTS (NCBI ptt file)||203, 330|
|CAC1423||CAC1423||Predicted dehydrogenase of short-chain alcohol dehydrogenase family, ortholog of YHDF B.subtilis (NCBI ptt file)||118, 300|
|CAC1486||CAC1486||Uncharacterized protein, ortholog of YKUS B.subtilis (NCBI ptt file)||118, 367|
|CAC1520||CAC1520||Hypothetical protein (NCBI ptt file)||118, 279|
|CAC1576||CAC1576||Predicted oxidoreductase, ortholog of GSP39 B.subtilis (NCBI ptt file)||188, 330|
|CAC1653||CAC1653||Predicted glycosyltransferases involved in cell wall biogenesis (NCBI ptt file)||73, 118|
|CAC1706||CAC1706||Phosphate permease (NCBI ptt file)||118, 245|
|CAC1707||CAC1707||Permease component of ATP-dependent phosphate uptake system (NCBI ptt file)||118, 245|
|CAC2058||CAC2058||Predicted membrane protein (NCBI ptt file)||39, 330|
|CAC2303||CAC2303||Stage V sporulation AE, SpoVAE (fragment) (NCBI ptt file)||22, 118|
|CAC2305||SpoVAC||Stage V sporulation AC, SpoVAC (NCBI ptt file)||110, 118|
|CAC2352||CAC2352||Hypothetical protein (NCBI ptt file)||279, 330|
|CAC2353||CAC2353||Hypothetical protein (NCBI ptt file)||279, 330|
|CAC2426||CAC2426||Uncharacterized conserved protein (NCBI ptt file)||263, 330|
|CAC2427||CAC2427||Uncharacterized conserved protein (NCBI ptt file)||263, 330|
|CAC2428||CAC2428||Activator of 2-hydroxyglutaryl-CoA dehydratase (NCBI ptt file)||263, 330|
|CAC2666||CAC2666||Hypothetical protein (NCBI ptt file)||300, 330|
|CAC2686||CAC2686||Possible maltodextrin glucosidase (NCBI ptt file)||203, 330|
|CAC2794||CAC2794||Transcriptional regulator, Lrp family (possible nitrite reductase regulator NirD) (NCBI ptt file)||300, 330|
|CAC2899||CAC2899||LysM repeats domain containing membrane protein (NCBI ptt file)||39, 330|
|CAC2903||CAC2903||LysM domain containing membrane protein (NCBI ptt file)||263, 330|
|CAC2981||CAC2981||Mannose-1-phosphate guanyltransferase (pyrophosphorylase domain and phosphomannomutase domain) (NCBI ptt file)||118, 123|
|CAC3016||CAC3016||Uncharacterized conserved membrane protein (NCBI ptt file)||95, 118|
|CAC3077||CAC3077||Uncharacterized FAD-dependent dehydrogenase (NCBI ptt file)||118, 142|
|CAC3213||CAC3213||Possible stage V sporulation protein B, predicted transporter (NCBI ptt file)||86, 118|
|CAC3230||CAC3230||Hydrogenase subunit (ferredoxin) (NCBI ptt file)||174, 330|
|CAC3245||CAC3245||Subtilisin like protease (two fused domains) (NCBI ptt file)||118, 330|
|CAC3278||CAC3278||Uncharacterized protein, containing cell adhesion domain and ChW-repeats (NCBI ptt file)||263, 330|
|CAC3357||CAC3357||Hypothetical protein (NCBI ptt file)||118, 174|
|CAC3402||CAC3402||Dipeptidyl aminopeptidase/acylaminoacyl-peptidase related protein (NCBI ptt file)||118, 317|
|CAC3403||CAC3403||Predicted membrane protein (NCBI ptt file)||118, 317|
|CAC3684||CAC3684||Polygalacturonase (NCBI ptt file)||22, 118|
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.
Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.
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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