Organism : Geobacter sulfurreducens | Module List :
methyl-accepting chemotaxis protein (VIMSS)
Functional Annotations (5)
|Methyl-accepting chemotaxis protein||cog/ cog|
|signal transducer activity||go/ molecular_function|
|signal transduction||go/ biological_process|
Regulation information for GSU0916(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 GSU0916
Module neighborhood information for GSU0916
|Gene||Common Name||Description||Module membership|
|GSU0048||GSU0048||integrase (NCBI)||287, 300|
|GSU0093||GSU0093||ABC transporter, ATP-binding/permease protein (VIMSS)||86, 186|
|GSU0265||GSU0265||membrane protein, putative (VIMSS)||21, 186|
|GSU0270||glmS||glucosamine--fructose-6-phosphate aminotransferase (isomerizing) (NCBI)||285, 287|
|GSU0411||fliG||flagellar motor switch protein FliG (NCBI)||14, 186|
|GSU0412||GSU0412||flagellar assembly protein fliH, putative (VIMSS)||186, 322|
|GSU0413||fliI||flagellum-specific ATP synthase FliI (NCBI)||186, 278|
|GSU0423||fliP||flagellar biosynthetic protein FliP (NCBI)||109, 186|
|GSU0547||mutS2||MutS2 family protein (NCBI)||252, 287|
|GSU0549||GSU0549||conserved domain protein (NCBI)||122, 287|
|GSU0574||GSU0574||membrane protein, putative (VIMSS)||96, 186|
|GSU0582||GSU0582||methyl-accepting chemotaxis protein (VIMSS)||281, 287|
|GSU0605||thiD||thiamine-phosphate pyrophosphorylase/phosphomethylpyrimidine kinase (NCBI)||99, 287|
|GSU0738||GSU0738||hypothetical protein (VIMSS)||97, 186|
|GSU0901||fragment||conserved domain protein (NCBI)||257, 287|
|GSU0916||GSU0916||methyl-accepting chemotaxis protein (VIMSS)||186, 287|
|GSU1029||GSU1029||methyl-accepting chemotaxis protein (VIMSS)||63, 287|
|GSU1101||GSU1101||sensory box histidine kinase (VIMSS)||252, 287|
|GSU1140||GSU1140||methyl-accepting chemotaxis protein (VIMSS)||186, 241|
|GSU1141||GSU1141||methyl-accepting chemotaxis protein (VIMSS)||186, 241|
|GSU1143||cheR-2||chemotaxis protein methyltransferase CheR (NCBI)||186, 241|
|GSU1383||dnaQ||exonuclease (NCBI)||287, 300|
|GSU1552||GSU1552||conserved hypothetical protein (VIMSS)||220, 287|
|GSU1567||htpX||peptidase, M48 family (NCBI)||78, 287|
|GSU1742||GSU1742||Na/Pi-cotransporter family protein (VIMSS)||287, 293|
|GSU2094||GSU2094||response regulator (VIMSS)||1, 287|
|GSU2300||GSU2300||hypothetical protein (VIMSS)||99, 287|
|GSU2441||GSU2441||conserved hypothetical protein (VIMSS)||287, 317|
|GSU2574||GSU2574||response regulator (VIMSS)||122, 287|
|GSU2581||GSU2581||sigma-54 dependent transcriptional regulator (VIMSS)||14, 186|
|GSU2594||GSU2594||ISGsu6, transposase OrfB (VIMSS)||287, 300|
|GSU2659||GSU2659||hypothetical protein (VIMSS)||183, 287|
|GSU2661||GSU2661||conserved hypothetical protein (VIMSS)||1, 287|
|GSU2759||GSU2759||potassium efflux system protein (VIMSS)||183, 287|
|GSU2901||GSU2901||membrane protein, putative (VIMSS)||186, 266|
|GSU2904||GSU2904||hypothetical protein (NCBI)||186, 257|
|GSU2942||GSU2942||methyl-accepting chemotaxis protein (VIMSS)||186, 224|
|GSU2984||znuC||permease component of zinc ABC transporter (Dmitry Rodionov)||96, 287|
|GSU2985||znuB||ATPase component of zinc ABC transporter (Dmitry Rodionov)||109, 186|
|GSU3047||flgI||flagellar P-ring protein FlgI (NCBI)||141, 186|
|GSU3048||flgH||flagellar L-ring protein FlgH (NCBI)||95, 186|
|GSU3052||flgG-2||flagellar basal-body rod protein FlgG (NCBI)||186, 312|
|GSU3054||GSU3054||ParA family protein (VIMSS)||186, 312|
|GSU3055||GSU3055||flagellar biosynthetic protein FlhF, putative (VIMSS)||186, 312|
|GSU3150||GSU3150||HPP family protein (NCBI)||26, 287|
|GSU3217||GSU3217||sigma-54 dependent DNA-binding response regulator (VIMSS)||92, 287|
|GSU3224||GSU3224||hypothetical protein (VIMSS)||287, 337|
|GSU3372||GSU3372||cardiolipin synthetase, putative (VIMSS)||287, 291|
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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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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