Organism : Geobacter sulfurreducens | Module List :
Na+/H+ antiporter family protein (VIMSS)
Functional Annotations (6)
|Na+/H+ antiporter||cog/ cog|
|sodium ion transport||go/ biological_process|
|regulation of pH||go/ biological_process|
|integral to membrane||go/ cellular_component|
|phosphopantetheine binding||go/ molecular_function|
|Methane metabolism||kegg/ kegg pathway|
Regulation information for GSU2303(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 GSU2303
Module neighborhood information for GSU2303
|Gene||Common Name||Description||Module membership|
|GSU0157||GSU0157||fibronectin type III domain protein (NCBI)||71, 222|
|GSU0496||GSU0496||efflux transporter, RND family, MFP subunit (NCBI)||20, 290|
|GSU0523||pabB||para-aminobenzoate synthase, component I (NCBI)||71, 104|
|GSU0691||GSU0691||translation initation factor SUI1, putative (NCBI)||71, 79|
|GSU0767||GSU0767||tia invasion determinant-related protein (VIMSS)||20, 288|
|GSU0811||ntrX||nitrogen regulation protein NtrX (NCBI)||71, 298|
|GSU0832||GSU0832||lipoprotein, putative (VIMSS)||71, 236|
|GSU0855||GSU0855||membrane protein, TerC family (NCBI)||59, 71|
|GSU0856||htpX||peptidase, M48 family (NCBI)||71, 321|
|GSU0921||rne||ribonuclease, Rne/Rng family protein (NCBI)||20, 99|
|GSU0922||GSU0922||ABC transporter, ATP-binding protein (VIMSS)||20, 283|
|GSU0923||loN-1||ATP-dependent protease La (NCBI)||20, 133|
|GSU0924||GSU0924||ABC transporter, permease protein, putative (VIMSS)||20, 133|
|GSU0926||GSU0926||mce-related protein (NCBI)||20, 95|
|GSU0927||GSU0927||peptidase, M16 family (NCBI)||20, 121|
|GSU0928||GSU0928||peptidase, M16 family (NCBI)||20, 57|
|GSU0929||GSU0929||conserved hypothetical protein (VIMSS)||20, 162|
|GSU1017||hpt||hypoxanthine phosphoribosyltransferase, putative (NCBI)||20, 77|
|GSU1024||cyd-4||cytochrome c3 (NCBI)||16, 20|
|GSU1394||GSU1394||spore coat protein-related protein (NCBI)||20, 57|
|GSU1401||dnaE||DNA polymerase III, alpha subunit (NCBI)||20, 241|
|GSU1402||accA||acetyl-CoA carboxylase, carboxyl transferase, alpha subunit (NCBI)||20, 321|
|GSU1568||GSU1568||conserved hypothetical protein (VIMSS)||71, 198|
|GSU1569||GSU1569||transcriptional regulator, CopG family (VIMSS)||71, 318|
|GSU1614||GSU1614||CoA-binding protein (VIMSS)||20, 326|
|GSU1837||GSU1837||peptidase, family M23/M37 domain protein (NCBI)||20, 46|
|GSU1875||ahcY||adenosylhomocysteinase (NCBI)||20, 46|
|GSU1877||fabK||oxidoreductase, 2-nitropropane dioxygenase family (NCBI)||71, 292|
|GSU1994||GSU1994||hypothetical protein (VIMSS)||71, 268|
|GSU2035||GSU2035||hypothetical protein (NCBI)||20, 138|
|GSU2041||GSU2041||sigma-54 dependent DNA-binding response regulator (VIMSS)||71, 104|
|GSU2087||gmhA||phosphoheptose isomerase (NCBI)||71, 108|
|GSU2122||GSU2122||TraG family protein (VIMSS)||71, 206|
|GSU2175||GSU2175||trfA-related protein (VIMSS)||71, 189|
|GSU2191||GSU2191||aldehyde ferredoxin oxidoreductase, tungsten-containing (VIMSS)||71, 206|
|GSU2201||GSU2201||cytochrome c family protein (NCBI)||20, 125|
|GSU2297||GSU2297||sensory box histidine kinase (VIMSS)||71, 181|
|GSU2302||GSU2302||trehalose-phosphatase, putative (VIMSS)||20, 189|
|GSU2303||GSU2303||Na+/H+ antiporter family protein (VIMSS)||20, 71|
|GSU2433||GSU2433||ATP-dependent protease, putative (VIMSS)||20, 49|
|GSU2483||kdpD||sensor histidine kinase KdpD (NCBI)||20, 49|
|GSU2693||GSU2693||response regulator (VIMSS)||71, 338|
|GSU2769||GSU2769||metallo-beta-lactamase family protein (VIMSS)||71, 206|
|GSU2883||GSU2883||cytochrome c family protein (VIMSS)||20, 46|
|GSU2954||acr3||arsenical-resistance protein (NCBI)||71, 146|
|GSU3100||hisD||histidinol dehydrogenase (NCBI)||71, 203|
|GSU3451||GSU3451||conserved hypothetical protein (VIMSS)||71, 201|
|GSU3463||gidB||glucose-inhibited division protein B (NCBI)||8, 71|
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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