Organism : Geobacter sulfurreducens | Module List :
Regulation information for GSU3128(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 GSU3128
|Gene||Common Name||Description||Module membership|
|GSU0061||GSU0061||hypothetical protein (VIMSS)||9, 95|
|GSU0116||GSU0116||transglycosylase (VIMSS)||95, 200|
|GSU0214||GSU0214||conserved hypothetical protein (VIMSS)||6, 95|
|GSU0357||GSU0357||cytochrome c family protein (VIMSS)||6, 95|
|GSU0362||GSU0362||hypothetical protein (VIMSS)||142, 183|
|GSU0436||pilT-3||twitching motility protein PilT (NCBI)||78, 183|
|GSU0446||GSU0446||conserved hypothetical protein TIGR00046 (VIMSS)||147, 183|
|GSU0533||GSU0533||cytochrome c family protein, putative (NCBI)||54, 95|
|GSU0541||polA||DNA polymerase I (NCBI)||164, 183|
|GSU0640||GSU0640||conserved hypothetical protein (VIMSS)||95, 158|
|GSU0656||ilvE||branched-chain amino acid aminotransferase (NCBI)||75, 183|
|GSU0671||rluC||ribosomal large subunit pseudouridine synthase C (NCBI)||26, 183|
|GSU0707||sugE||sugE protein (NCBI)||95, 234|
|GSU0751||GSU0751||conserved hypothetical protein (VIMSS)||147, 183|
|GSU0806||citG||ATP:dephospho-CoA triphosphoribosyl transferase (NCBI)||95, 133|
|GSU0825||GSU0825||pirin family protein (VIMSS)||126, 183|
|GSU0843||GSU0843||NADH oxidase, putative (VIMSS)||9, 95|
|GSU0845||GSU0845||Rieske 2Fe-2S family protein (VIMSS)||9, 95|
|GSU0890||ligA||DNA ligase, NAD-dependent (NCBI)||183, 281|
|GSU0894||ppiB||peptidyl-prolyl cis-trans isomerase, cyclophilin-type (NCBI)||183, 245|
|GSU0926||GSU0926||mce-related protein (NCBI)||20, 95|
|GSU0952||GSU0952||GGDEF domain protein (NCBI)||26, 183|
|GSU1067||GSU1067||conserved hypothetical protein (VIMSS)||156, 183|
|GSU1255||GSU1255||conserved hypothetical protein (NCBI)||95, 104|
|GSU1256||GSU1256||conserved domain protein (NCBI)||6, 95|
|GSU1298||GSU1298||methyl-accepting chemotaxis protein (VIMSS)||126, 183|
|GSU1443||GSU1443||sensor histidine kinase/response regulator (VIMSS)||183, 191|
|GSU1527||GSU1527||conserved hypothetical protein (VIMSS)||147, 183|
|GSU1772||ctpA-2||carboxy-terminal processing protease (NCBI)||25, 183|
|GSU1809||ftsH-2||cell division protein FtsH (NCBI)||183, 207|
|GSU1844||GSU1844||IPT/TIG domain protein, putative (VIMSS)||9, 95|
|GSU1870||GSU1870||GGDEF domain protein (VIMSS)||183, 335|
|GSU2102||GSU2102||pyruvate formate-lyase-activating enzyme, putative (VIMSS)||126, 183|
|GSU2199||GSU2199||conserved hypothetical protein (VIMSS)||95, 273|
|GSU2414||GSU2414||membrane protein, putative (VIMSS)||164, 183|
|GSU2464||GSU2464||hypothetical protein (VIMSS)||156, 183|
|GSU2509||GSU2509||glycosyl transferase, group 2 family protein (VIMSS)||9, 95|
|GSU2515||GSU2515||cytochrome c family protein, putative (NCBI)||9, 95|
|GSU2561||GSU2561||conserved domain protein (NCBI)||95, 193|
|GSU2587||GSU2587||transcriptional regulator, MarR family (VIMSS)||140, 183|
|GSU2640||GSU2640||hypothetical protein (VIMSS)||66, 95|
|GSU2641||GSU2641||hypothetical protein (VIMSS)||66, 95|
|GSU2659||GSU2659||hypothetical protein (VIMSS)||183, 287|
|GSU2759||GSU2759||potassium efflux system protein (VIMSS)||183, 287|
|GSU2775||GSU2775||hypothetical protein (VIMSS)||9, 95|
|GSU2787||GSU2787||transcriptional regulator, LysR family (VIMSS)||95, 224|
|GSU2896||GSU2896||ankyrin-related protein (VIMSS)||6, 95|
|GSU3000||GSU3000||cbiX protein (NCBI)||183, 265|
|GSU3048||flgH||flagellar L-ring protein FlgH (NCBI)||95, 186|
|GSU3071||murD||UDP-N-acetylmuramoylalanine--D-glutamate ligase (NCBI)||95, 264|
|GSU3108||rho||transcription termination factor Rho (NCBI)||183, 335|
|GSU3128||GSU3128||hypothetical protein (VIMSS)||95, 183|
|GSU3160||rluC||RNA pseudouridine synthase family protein (NCBI)||42, 183|
|GSU3203||GSU3203||outer membrane lipoprotein carrier protein LolA, putative (NCBI)||104, 183|
|GSU3238||GSU3238||Rieske 2Fe-2S family protein (VIMSS)||95, 264|
|GSU3314||GSU3314||lipoprotein, putative (VIMSS)||164, 183|
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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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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