Organism : Geobacter sulfurreducens | Module List :
Regulation information for GSU3184(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 GSU3184
Module neighborhood information for GSU3184
|Gene||Common Name||Description||Module membership|
|GSU0044||GSU0044||salmonella virulence plasmid 65kDa B protein /YD repeat protein (NCBI)||274, 300|
|GSU0045||GSU0045||hypothetical protein (VIMSS)||232, 300|
|GSU0048||GSU0048||integrase (NCBI)||287, 300|
|GSU0105||GSU0105||cytochrome c family protein, putative (NCBI)||180, 181|
|GSU0107||spo0J||parB-like domain protein (NCBI)||147, 181|
|GSU0223||GSU0223||protoheme IX farnesyl transferase, putative (VIMSS)||257, 300|
|GSU0369||GSU0369||FlhB domain protein, putative (NCBI)||293, 300|
|GSU0422||fliN||flagellar motor switch protein FliN (NCBI)||181, 234|
|GSU0515||GSU0515||universal stress protein family (VIMSS)||69, 181|
|GSU0595||GSU0595||hypothetical protein (NCBI)||300, 337|
|GSU0758||GSU0758||membrane protein, putative (VIMSS)||181, 278|
|GSU1039||GSU1039||sigma-54 dependent DNA-binding response regulator (VIMSS)||181, 269|
|GSU1047||GSU1047||conserved hypothetical protein (VIMSS)||181, 253|
|GSU1114||GSU1114||TPR domain protein (VIMSS)||181, 267|
|GSU1172||mviN||virulence factor mviN protein (NCBI)||295, 300|
|GSU1181||GSU1181||hypothetical protein (VIMSS)||176, 181|
|GSU1216||cydC||transport ATP-binding protein CydC (NCBI)||8, 181|
|GSU1222||GSU1222||histone deacetylase/AcuC/AphA family protein (VIMSS)||106, 181|
|GSU1240||GSU1240||hypothetical protein (VIMSS)||176, 181|
|GSU1270||pyrR||pyrimidine operon regulatory protein PyrR (NCBI)||281, 300|
|GSU1281||nikO||component of nickel ABC transport system (Dmitry Rodionov)||181, 278|
|GSU1310||GSU1310||pyridine nucleotide-disulfide oxidoreductase (Regina ONeil)||181, 205|
|GSU1319||GSU1319||sensor histidine kinase (VIMSS)||106, 181|
|GSU1329||gltX||tRNA synthetases class I (E and Q), catalytic domain protein (NCBI)||15, 300|
|GSU1383||dnaQ||exonuclease (NCBI)||287, 300|
|GSU1446||GSU1446||radical SAM domain protein (NCBI)||181, 207|
|GSU1539||xth||exodeoxyribonuclease III (NCBI)||274, 300|
|GSU1545||GSU1545||transporter, LysE family (VIMSS)||181, 338|
|GSU1565||GSU1565||hypothetical protein (VIMSS)||276, 300|
|GSU1573||GSU1573||CAAX amino terminal protease family protein (NCBI)||181, 253|
|GSU1680||GSU1680||conserved hypothetical protein (VIMSS)||59, 300|
|GSU1703||pfk||6-phosphofructokinase (NCBI)||204, 300|
|GSU1715||GSU1715||hypothetical protein (VIMSS)||51, 181|
|GSU1740||GSU1740||cytochrome c family protein, putative (VIMSS)||69, 181|
|GSU2080||GSU2080||rod shape-determining protein MreD, putative (VIMSS)||137, 300|
|GSU2116||GSU2116||hypothetical protein (VIMSS)||181, 253|
|GSU2117||GSU2117||hypothetical protein (VIMSS)||181, 278|
|GSU2163||GSU2163||hypothetical protein (VIMSS)||181, 278|
|GSU2166||GSU2166||hypothetical protein (VIMSS)||1, 300|
|GSU2177||GSU2177||hypothetical protein (VIMSS)||113, 181|
|GSU2204||GSU2204||cytochrome c family protein, putative (NCBI)||300, 327|
|GSU2205||GSU2205||hypothetical protein (VIMSS)||300, 337|
|GSU2293||GSU2293||hypothetical protein (VIMSS)||181, 338|
|GSU2297||GSU2297||sensory box histidine kinase (VIMSS)||71, 181|
|GSU2312||GSU2312||sulfate transporter family protein (VIMSS)||130, 181|
|GSU2336||otsB||trehalose-phosphatase (NCBI)||296, 300|
|GSU2472||vapC||virulence associated protein C (NCBI)||181, 193|
|GSU2474||GSU2474||hypothetical protein (VIMSS)||88, 181|
|GSU2540||GSU2540||transcriptional regulator, Cro/CI family (VIMSS)||181, 304|
|GSU2578||cheW-9||purine-binding chemotaxis protein CheW (NCBI)||79, 300|
|GSU2592||GSU2592||hypothetical protein (VIMSS)||68, 300|
|GSU2593||GSU2593||ISGsu6, transposase OrfA (VIMSS)||234, 300|
|GSU2594||GSU2594||ISGsu6, transposase OrfB (VIMSS)||287, 300|
|GSU2664||GSU2664||outer membrane efflux protein (VIMSS)||181, 244|
|GSU2716||sfsA||sugar fermentation stimulation protein (NCBI)||226, 300|
|GSU2890||GSU2890||cytochrome c biogenesis protein, CcmF/CcyK/CcsA family (VIMSS)||130, 300|
|GSU2927||GSU2927||cytochrome c, putative (NCBI)||181, 327|
|GSU2957||GSU2957||thioredoxin family protein (VIMSS)||146, 300|
|GSU3184||GSU3184||hypothetical protein (VIMSS)||181, 300|
|GSU3186||GSU3186||conserved hypothetical protein (VIMSS)||213, 300|
|GSU3264||GSU3264||membrane protein, putative (VIMSS)||295, 300|
|GSU3286||hemD||uroporphyrinogen III synthase/methyltransferase (NCBI)||89, 300|
|GSU3361||GSU3361||transglutaminase domain protein (NCBI)||180, 181|
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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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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