Organism : Clostridium acetobutylicum | Module List :
CheX protein (uncharacterized ORF in chemotaxis operon) (NCBI ptt file)
Functional Annotations (1)
|Predicted inhibitor of MCP methylation, homolog of CheC||cog/ cog|
Regulation information for CAC0586(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 CAC0586
|Predicted inhibitor of MCP methylation, homolog of CheC||cog/ cog|
Module neighborhood information for CAC0586
|Gene||Common Name||Description||Module membership|
|CAC0053||CAC0053||Hypothetical protein (NCBI ptt file)||70, 86|
|CAC0414||CAC0414||Hypothetical protein (NCBI ptt file)||211, 249|
|CAC0442||CAC0442||Permease, putative chloride channel (NCBI ptt file)||70, 214|
|CAC0448||feoB||Ferrous iron transport protein B (feoB-2) (NCBI ptt file)||70, 227|
|CAC0525||CAC0525||Sensory transduction histidine kinase (HisKA and HATPase_c domains) (NCBI ptt file)||70, 73|
|CAC0527||CAC0527||Predicted permease, domain duplication (NCBI ptt file)||70, 154|
|CAC0528||CAC0528||ABC transporter, ATPase component (two ATPase domains) (NCBI ptt file)||249, 281|
|CAC0542||CAC0542||Methyl-accepting chemotaxis protein (NCBI ptt file)||70, 285|
|CAC0586||CAC0586||CheX protein (uncharacterized ORF in chemotaxis operon) (NCBI ptt file)||70, 249|
|CAC0757||CAC0757||Predicted membrane protein (NCBI ptt file)||70, 223|
|CAC1146||CAC1146||Hypothetical protein (NCBI ptt file)||16, 249|
|CAC1149||CAC1149||Hypothetical protein (NCBI ptt file)||16, 249|
|CAC1150||CAC1150||Hypothetical protein (NCBI ptt file)||16, 249|
|CAC1153||CAC1153||Hypothetical protein (NCBI ptt file)||16, 249|
|CAC1155||CAC1155||Hypothetical protein (NCBI ptt file)||16, 249|
|CAC1157||CAC1157||Hypothetical protein (NCBI ptt file)||16, 249|
|CAC1159||CAC1159||Hypothetical protein (NCBI ptt file)||16, 249|
|CAC1392||purF||Glutamine phosphoribosylpyrophosphate amidotransferase (NCBI ptt file)||193, 249|
|CAC1395||purH||AICAR transformylase/IMP cyclohydrolase (NCBI ptt file)||193, 249|
|CAC1396||purD||Phosphoribosylamine-glycine ligase (NCBI ptt file)||249, 360|
|CAC1570||bsaA||Glutathione peroxidase (NCBI ptt file)||9, 70|
|CAC1571||CAC1571||Glutathione peroxidase (NCBI ptt file)||70, 214|
|CAC1590||CAC1590||2-oxoglutarate/malate translocator (NCBI ptt file)||66, 249|
|CAC1595||CAC1595||Integrase/recombinase, XerC/XerD family (NCBI ptt file)||249, 360|
|CAC1603||CAC1603||Diverged enzyme related to 2'-5' RNA ligase, ortholog YJCG B.subtilis (NCBI ptt file)||70, 83|
|CAC1613||CAC1613||ABC-type multidrug/protein/lipid transport system, membrane ATPase component (NCBI ptt file)||76, 249|
|CAC1655||purQ/purL||bifunctional enzyme phosphoribosylformylglycinamidine (FGAM) synthase (synthetase domain/glutamine amidotransferase domain) (NCBI ptt file)||214, 249|
|CAC1966||CAC1966||Surface-layer related glycoprotein (NCBI ptt file)||70, 291|
|CAC2541||CAC2541||Reductase/isomerase/elongation factor common domain (NCBI ptt file)||70, 291|
|CAC2545||CAC2545||Hypothetical protein (NCBI ptt file)||70, 326|
|CAC2692||CAC2692||O-Acetyltransferase, from isoleucine patch superfamily (NCBI ptt file)||70, 266|
|CAC2830||CAC2830||Acylphosphatases, ACYP (NCBI ptt file)||70, 92|
|CAC3021||CAC3021||Possible phosphoglycerate mutase (NCBI ptt file)||70, 218|
|CAC3284||CAC3284||Uncharacterized conserved protein, DegV family (NCBI ptt file)||49, 70|
|CAC3410||CAC3410||HD-GYP domain (HD superfamily hydrolase) (NCBI ptt file)||70, 72|
|CAC3527||CAC3527||Ferredoxin (NCBI ptt file)||66, 249|
|CAC3622||CAC3622||Possible subunit of benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase (NCBI ptt file)||193, 249|
|CAC3625||CAC3625||Fe-S oxidoreductase of MoaA family (NCBI ptt file)||193, 249|
|CAC3626||mtrA||GTP cyclohydrolase I (NCBI ptt file)||193, 249|
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.
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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
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