Organism : Geobacter sulfurreducens | Module List :
Regulation information for GSU2642(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|
Module neighborhood information for GSU2642
|Gene||Common Name||Description||Module membership|
|GSU0088||GSU0088||heterodisulfide reductase subunit (VIMSS)||169, 214|
|GSU0111||atpA||ATP synthase F1, alpha subunit (NCBI)||10, 169|
|GSU0197||GSU0197||oxidoreductase, short chain dehydrogenase/reductase family (VIMSS)||80, 169|
|GSU0298||GSU0298||sigma-54 dependent DNA-binding response regulator, interruption-C (VIMSS)||116, 169|
|GSU0334||atpB||ATP synthase F0, A subunit (NCBI)||62, 136|
|GSU0871||GSU0871||radical SAM domain protein/B12 binding domain protein (NCBI)||50, 169|
|GSU1314||GSU1314||membrane protein, putative (VIMSS)||75, 136|
|GSU1375||GSU1375||hypothetical protein (VIMSS)||169, 225|
|GSU1496||GSU1496||pilin domain protein (VIMSS)||117, 169|
|GSU1497||GSU1497||hypothetical protein (VIMSS)||117, 169|
|GSU1599||rpmF||ribosomal protein L32 (NCBI)||62, 169|
|GSU1626||GSU1626||transcriptional regulator, GntR family (VIMSS)||136, 154|
|GSU1651||fbP-1||fructose-1,6-bisphosphatase (NCBI)||136, 154|
|GSU1660||acnB||aconitate hydratase 2 (NCBI)||101, 169|
|GSU1738||GSU1738||indolepyruvate ferredoxin oxidoreductase, beta subunit (VIMSS)||112, 136|
|GSU1757||rimI||ribosomal-protein-alanine acetyltransferase (VIMSS)||136, 208|
|GSU1804||pdxJ||pyridoxal phosphate biosynthetic protein PdxJ (NCBI)||67, 136|
|GSU1884||GSU1884||conserved hypothetical protein (VIMSS)||136, 263|
|GSU1886||yfiA||ribosomal subunit interface protein (NCBI)||169, 238|
|GSU1902||leuD||3-isopropylmalate dehydratase, small subunit, putative (NCBI)||101, 169|
|GSU1903||leuC||3-isopropylmalate dehydratase, large subunit, putative (NCBI)||136, 197|
|GSU2028||GSU2028||type IV pilus biogenesis protein PilQ (VIMSS)||76, 136|
|GSU2029||GSU2029||lipoprotein, putative (VIMSS)||76, 136|
|GSU2237||rpoZ||DNA-directed RNA polymerase, omega subunit (NCBI)||169, 228|
|GSU2519||GSU2519||(R)-2-hydroxyglutaryl-CoA dehydratase beta-subunit, putative (NCBI)||136, 168|
|GSU2642||GSU2642||cytochrome c family protein (NCBI)||136, 169|
|GSU2643||GSU2643||cytochrome c family protein (NCBI)||18, 136|
|GSU2644||GSU2644||hypothetical protein (VIMSS)||136, 330|
|GSU2645||GSU2645||cytochrome c family protein (NCBI)||169, 215|
|GSU2998||GSU2998||nitroimidazole resistance protein, putative (VIMSS)||89, 169|
|GSU3005||thiC-2||thiamine biosynthesis protein ThiC (NCBI)||101, 169|
|GSU3007||GSU3007||phosphoglycerate mutase family, putative (VIMSS)||101, 169|
|GSU3009||cobT||nicotinate-nucleotide--dimethylbenzimidazolephosphoribosyltransferase (NCBI)||101, 169|
|GSU3278||GSU3278||hypothetical protein (VIMSS)||169, 276|
|GSU3392||GSU3392||branched-chain amino acid ABC transporter, ATP-binding protein (NCBI)||80, 136|
|GSU3401||GSU3401||branched-chain amino acid ABC transporter, periplasmic amino acid-binding protein, putative (NCBI)||117, 169|
|GSU3402||GSU3402||hypothetical protein (VIMSS)||117, 169|
|GSU3403||GSU3403||hypothetical protein (VIMSS)||117, 169|
|GSU3406||GSU3406||amino acid ABC transporter, periplasmic amino acid-binding protein (NCBI)||117, 169|
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.
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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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