Organism : Geobacter sulfurreducens | Module List :
heavy metal efflux pump, CzcA family (VIMSS)
Functional Annotations (6)
|Putative silver efflux pump||cog/ cog|
|cation transport||go/ biological_process|
|cation transmembrane transporter activity||go/ molecular_function|
|integral to membrane||go/ cellular_component|
|Two-component system||kegg/ kegg pathway|
Regulation information for GSU1332(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 GSU1332
Module neighborhood information for GSU1332
|Gene||Common Name||Description||Module membership|
|GSU0182||GSU0182||lipoprotein, putative (VIMSS)||46, 292|
|GSU0183||GSU0183||lipoprotein, putative (VIMSS)||46, 325|
|GSU0210||GSU0210||conserved hypothetical protein (VIMSS)||46, 91|
|GSU0211||GSU0211||ABC transporter, permease protein, putative (VIMSS)||46, 321|
|GSU0492||xerD||site-specific recombinase, phage integrase family (NCBI)||46, 49|
|GSU0844||GSU0844||potassium uptake protein, Trk family (VIMSS)||46, 97|
|GSU0862||folD-2||folD bifunctional protein (NCBI)||46, 126|
|GSU0874||GSU0874||hypothetical protein (VIMSS)||46, 321|
|GSU1060||GSU1060||hypothetical protein (VIMSS)||269, 341|
|GSU1190||GSU1190||conserved hypothetical protein (VIMSS)||46, 253|
|GSU1250||GSU1250||sigma-54 dependent DNA-binding response regulator (VIMSS)||46, 206|
|GSU1331||GSU1331||efflux transporter, RND family, MFP subunit (NCBI)||165, 341|
|GSU1332||GSU1332||heavy metal efflux pump, CzcA family (VIMSS)||46, 341|
|GSU1339||GSU1339||hypothetical protein (NCBI)||206, 341|
|GSU1340||GSU1340||ABC transporter, permease protein (VIMSS)||206, 341|
|GSU1341||GSU1341||ABC transporter, ATP-binding protein (VIMSS)||184, 341|
|GSU1355||GSU1355||ISGsu7, transposase OrfA (VIMSS)||335, 341|
|GSU1403||rluB||ribosomal large subunit pseudouridine synthase B (NCBI)||46, 201|
|GSU1837||GSU1837||peptidase, family M23/M37 domain protein (NCBI)||20, 46|
|GSU1875||ahcY||adenosylhomocysteinase (NCBI)||20, 46|
|GSU2150||GSU2150||hypothetical protein (VIMSS)||46, 142|
|GSU2287||GSU2287||response regulator (VIMSS)||11, 46|
|GSU2288||GSU2288||sensor histidine kinase (VIMSS)||46, 77|
|GSU2289||GSU2289||nicotinate phosphoribosyltransferase, putative (NCBI)||46, 79|
|GSU2290||pncA||pyrazinamidase/nicotinamidase, putative (NCBI)||46, 321|
|GSU2476||GSU2476||TPR domain protein (VIMSS)||46, 220|
|GSU2493||GSU2493||NHL repeat domain protein (NCBI)||9, 341|
|GSU2494||GSU2494||cytochrome c family protein (VIMSS)||46, 178|
|GSU2497||GSU2497||lipoprotein, putative (VIMSS)||206, 341|
|GSU2498||GSU2498||lipoprotein, putative (VIMSS)||206, 341|
|GSU2499||GSU2499||hypothetical protein (VIMSS)||66, 341|
|GSU2501||GSU2501||cytochrome c family protein (NCBI)||66, 341|
|GSU2502||GSU2502||spermine/spermidine synthase family protein (VIMSS)||141, 341|
|GSU2505||GSU2505||NHL repeat domain protein (VIMSS)||66, 341|
|GSU2506||GSU2506||sensory box protein/sigma-54 dependent DNA-binding response regulator (NCBI)||97, 341|
|GSU2507||GSU2507||sensor histidine kinase (NCBI)||299, 341|
|GSU2508||GSU2508||TPR domain protein (NCBI)||6, 341|
|GSU2529||fusA-2||translation elongation factor G (NCBI)||9, 46|
|GSU2747||GSU2747||hypothetical protein (VIMSS)||110, 341|
|GSU2883||GSU2883||cytochrome c family protein (VIMSS)||20, 46|
|GSU2975||GSU2975||inorganic pyrophosphatase, manganese-dependent, putative (VIMSS)||46, 220|
|GSU3348||hslO||chaperonin, 33 kDa family (NCBI)||46, 321|
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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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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