Organism : Clostridium acetobutylicum | Module List :
Multimeric flavodoxin WrbA fused to cytochrome c-like domain (NCBI ptt file)
Functional Annotations (1)
|Multimeric flavodoxin WrbA||cog/ cog|
Regulation information for CAC2528(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 CAC2528
|Multimeric flavodoxin WrbA||cog/ cog|
Module neighborhood information for CAC2528
|Gene||Common Name||Description||Module membership|
|CAC0071||CAC0071||Uncharacterized conserved protein, YTFE E.coli ortholog (NCBI ptt file)||24, 108|
|CAC0078||agrB||Accessory gene regulator protein B (NCBI ptt file)||7, 178|
|CAC0193||CAC0193||Uncharacterized conserved membrane protein, affecting LPS biosynthesis (NCBI ptt file)||7, 174|
|CAC0194||CAC0194||Glycosyltransferase involved in cell wall biogenesis (NCBI ptt file)||7, 174|
|CAC0202||CAC0202||Hydrolase of the alpha/beta superfamily (NCBI ptt file)||24, 288|
|CAC0203||CAC0203||Flavodoxin (NCBI ptt file)||24, 288|
|CAC0326||CAC0326||ATPase related to the helicase subunit of Holliday junction resolvase (NCBI ptt file)||24, 89|
|CAC0555||CAC0555||Predicted membrane protein (NCBI ptt file)||7, 134|
|CAC0598||gerKC||Spore germination protein, gerKC (NCBI ptt file)||24, 145|
|CAC0625||CAC0625||Possible periplasmic aspartyl protease (NCBI ptt file)||24, 266|
|CAC0741||CAC0741||Methyl-accepting chemotaxis protein (NCBI ptt file)||24, 285|
|CAC0792||CAC0792||D-amino acid aminotransferase (NCBI ptt file)||7, 178|
|CAC0805||CAC0805||Methyl-accepting chemotaxis protein (NCBI ptt file)||24, 207|
|CAC0921||CAC0921||Metal-dependent amidohydrolase (NCBI ptt file)||24, 108|
|CAC1351||CAC1351||Periplasmic sugar-binding protein (NCBI ptt file)||24, 267|
|CAC2407||CAC2407||CheY-like receiver domain of response regulator (NCBI ptt file)||7, 155|
|CAC2408||CAC2408||Glycosyltransferase (NCBI ptt file)||7, 155|
|CAC2528||CAC2528||Multimeric flavodoxin WrbA fused to cytochrome c-like domain (NCBI ptt file)||7, 24|
|CAC2531||CAC2531||S-adenosylmethionine-dependent methyltransferase (NCBI ptt file)||7, 200|
|CAC2592||CAC2592||6-pyruvoyl-tetrahydropterin synthase related domain; conserved membrane protein (NCBI ptt file)||24, 240|
|CAC2722||CAC2722||RCC1 repeats protein (beta propeller fold) (NCBI ptt file)||7, 200|
|CAC2812||CAC2812||Hypothetical protein (NCBI ptt file)||24, 115|
|CAC2898||spoIIR||Stage II sporulation protein R (NCBI ptt file)||24, 179|
|CAC2919||CAC2919||Hypothetical protein (NCBI ptt file)||24, 73|
|CAC3301||gerKB||Spore germination protein GerKB, membrane protein (NCBI ptt file)||24, 240|
|CAC3324||CAC3324||Predicted transcriptional regulator (NCBI ptt file)||24, 227|
|CAC3329||CAC3329||Putative Mn transporter, NRAMP family (NCBI ptt file)||24, 40|
|CAC3331||CAC3331||Alanine racemase (NCBI ptt file)||24, 353|
|CAC3355||CAC3355||Polyketide synthase pksE (short-chain alcohol dehydrogenase,acyl-carrier-protein S-malonyltransferase,3-oxoacyl-(acyl-carrier-protein) synthase I domains) (NCBI ptt file)||7, 178|
|CAC3408||CAC3408||NADH oxidase (two distinct flavin oxidoreductase domains) (NCBI ptt file)||7, 178|
|CAC3409||alsR||Transcriptional regulators, LysR family (NCBI ptt file)||7, 178|
|CAC3558||CAC3558||Probable S-layer protein (NCBI ptt file)||7, 18|
|CAC3610||CAC3610||ABC-type MDR transport system, permease component (NCBI ptt file)||24, 150|
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;
- 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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