Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC0040(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 CAC0040
Module neighborhood information for CAC0040
|Gene||Common Name||Description||Module membership|
|CAC0040||CAC0040||Uncharacterized small conserved protein, homolog of yfjA/yukE B.subtilis (NCBI ptt file)||82, 251|
|CAC0168||CAC0168||T-RNA-processing ribonuclease BN (NCBI ptt file)||82, 207|
|CAC0208||CAC0208||Predicted membrane protein; CF-20 family (NCBI ptt file)||82, 302|
|CAC0209||CAC0209||Predicted membrane protein; CF-20 family (NCBI ptt file)||82, 366|
|CAC0279||CAC0279||Peptidil-prolyl cis-trans isomerase (NCBI ptt file)||251, 348|
|CAC0290||CAC0290||Sensory transduction histidine kinases (NCBI ptt file)||82, 91|
|CAC0386||licC||PTS cellobiose-specific component IIC (NCBI ptt file)||82, 285|
|CAC0413||CAC0413||Uncharacterized small conserved protein, homolog of YUKE/YFJA (NCBI ptt file)||242, 251|
|CAC0539||manB||Beta-mannanase ManB, contains ChW-repeats (NCBI ptt file)||82, 251|
|CAC0573||CAC0573||Uncharacterized protein, homolog YvqG B.subtilis (NCBI ptt file)||102, 251|
|CAC0624||CAC0624||Hypothetical protein (NCBI ptt file)||122, 251|
|CAC0630||CAC0630||Peptide chain ralease factor 3 (RF-3) (NCBI ptt file)||82, 160|
|CAC0633||CAC0633||Predicted phosphatase (NCBI ptt file)||82, 151|
|CAC0706||CAC0706||Endo-1,4-beta glucanase (fused to two ricin-B-like domains) (NCBI ptt file)||170, 251|
|CAC0783||CAC0783||Uncharacterized low-complexity protein (NCBI ptt file)||82, 251|
|CAC0784||CAC0784||ATP-dependent RNA helicase, superfamily II (NCBI ptt file)||82, 251|
|CAC0806||CAC0806||Hypothetical protein (NCBI ptt file)||218, 251|
|CAC0819||CAC0819||Phosphoribosylpyrophosphate synthetase (NCBI ptt file)||215, 251|
|CAC1083||CAC1083||Predicted membrane-associated metal-binding protein (NCBI ptt file)||185, 251|
|CAC1241||radc||RadC protein ortholog (NCBI ptt file)||3, 251|
|CAC1301||CAC1301||Predicted membrane protein (NCBI ptt file)||10, 251|
|CAC1615||CAC1615||Predicted glycosyltransferase (NCBI ptt file)||69, 82|
|CAC1620||CAC1620||Small acid-soluble spore protein (NCBI ptt file)||251, 265|
|CAC1716||CAC1716||Uncharacterized stress-induced protein, YicC family (NCBI ptt file)||3, 251|
|CAC1753||CAC1753||Uncharacterized conserved protein, YLXM B.subtilis ortholog (NCBI ptt file)||251, 302|
|CAC1754||ffh||Signal recognition particle GTPase Ffh (NCBI ptt file)||251, 302|
|CAC1786||codY||Transcriptional regulator, CodY B.subtilis ortholog (NCBI ptt file)||215, 251|
|CAC2174||CAC2174||Glycosyltransferase (NCBI ptt file)||82, 346|
|CAC2244||CAC2244||HAD superfamily hydrolases, YKRA B.subtilis ortholog (NCBI ptt file)||216, 251|
|CAC2253||CAC2253||Membrane-associated sensory histidine kinase-like ATPase (NCBI ptt file)||82, 106|
|CAC2323||CAC2323||Predicted membrane protein (NCBI ptt file)||5, 82|
|CAC2324||CAC2324||Glycosyltransferase (NCBI ptt file)||82, 215|
|CAC2338||CAC2338||Lysine decarboxylase (NCBI ptt file)||82, 285|
|CAC2432||CAC2432||Predicted permease (NCBI ptt file)||82, 106|
|CAC2601||CAC2601||S-adenosylmethionine decarboxylase (NCBI ptt file)||82, 225|
|CAC2912||araN||Sugar-binding periplasmic protein (NCBI ptt file)||82, 235|
|CAC2913||CAC2913||Hypothetical protein (NCBI ptt file)||82, 235|
|CAC3062||CAC3062||CPSB/CAPC ortholog, PHP family hydrolase (NCBI ptt file)||238, 251|
|CAC3212||CAC3212||Fusion of Uroporphyrinogen-III methylase related protein and MAZG family protein, YABN B.subtilis ortholog (NCBI ptt file)||82, 302|
|CAC3221||prs||Phosphoribosylpyrophosphate synthetase (NCBI ptt file)||109, 251|
|CAC3260||asnS||Aspartyl/asparaginyl-tRNA synthetase (NCBI ptt file)||82, 292|
|CAC3668||CAC3668||MDR-type permease (NCBI ptt file)||82, 251|
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;
- 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.
- 2. Source gene
- 3. Target genes (other module members)
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