Organism : Geobacter sulfurreducens | Module List :
nickel-dependent hydrogenase, large subunit (VIMSS)
Functional Annotations (5)
|Ni,Fe-hydrogenase I large subunit||cog/ cog|
|electron transport||go/ biological_process|
|ferredoxin hydrogenase activity||go/ molecular_function|
|nickel ion binding||go/ molecular_function|
|hydrogenase (acceptor) activity||go/ molecular_function|
Regulation information for GSU0122(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 GSU0122
Module neighborhood information for GSU0122
|Gene||Common Name||Description||Module membership|
|GSU0057||GSU0057||CRISPR-associated protein Cas1/Cas4 (NCBI)||157, 195|
|GSU0058||GSU0058||CRISPR-associated protein Cas2, putative (NCBI)||157, 195|
|GSU0122||GSU0122||nickel-dependent hydrogenase, large subunit (VIMSS)||21, 157|
|GSU0132||GSU0132||conserved hypothetical protein (VIMSS)||155, 157|
|GSU0178||GSU0178||conserved hypothetical protein (VIMSS)||157, 202|
|GSU0218||GSU0218||conserved hypothetical protein (VIMSS)||21, 266|
|GSU0265||GSU0265||membrane protein, putative (VIMSS)||21, 186|
|GSU0395||GSU0395||conserved hypothetical protein (VIMSS)||94, 157|
|GSU0428||GSU0428||lipoprotein, putative (VIMSS)||21, 278|
|GSU0433||GSU0433||clpB protein, putative (NCBI)||21, 96|
|GSU0583||GSU0583||methyl-accepting chemotaxis protein (VIMSS)||100, 157|
|GSU0692||GSU0692||carbohydrate kinase, PfkB family (VIMSS)||9, 157|
|GSU0693||GSU0693||sensory box histidine kinase (VIMSS)||103, 157|
|GSU0760||GSU0760||hypothetical protein (VIMSS)||151, 157|
|GSU0837||GSU0837||response regulator (VIMSS)||21, 155|
|GSU0848||GSU0848||ferredoxin family protein, putative (VIMSS)||21, 189|
|GSU0849||GSU0849||conserved hypothetical protein (VIMSS)||21, 157|
|GSU0942||suhB||inositol-1-monophosphatase (NCBI)||157, 193|
|GSU1015||GSU1015||hypothetical protein (VIMSS)||21, 189|
|GSU1036||GSU1036||sensor histidine kinase (VIMSS)||53, 157|
|GSU1049||GSU1049||conserved hypothetical protein (NCBI)||21, 272|
|GSU1050||GSU1050||sensory box histidine kinase (VIMSS)||21, 272|
|GSU1056||GSU1056||conserved hypothetical protein TIGR00149 (VIMSS)||21, 133|
|GSU1057||GSU1057||hypothetical protein (VIMSS)||21, 133|
|GSU1058||sucC||succinyl-CoA synthase, beta subunit (NCBI)||21, 133|
|GSU1066||GSU1066||hypothetical protein (NCBI)||4, 157|
|GSU1185||GSU1185||conserved hypothetical protein (VIMSS)||41, 157|
|GSU1299||cheW||purine-binding chemotaxis protein CheW (NCBI)||59, 157|
|GSU1415||GSU1415||response regulator (VIMSS)||21, 157|
|GSU1685||GSU1685||HD domain protein (NCBI)||21, 38|
|GSU2349||GSU2349||hypothetical protein (VIMSS)||21, 45|
|GSU2512||GSU2512||hypothetical protein (VIMSS)||21, 180|
|GSU2562||sixA||phosphohistidine phosphatase SixA (NCBI)||140, 157|
|GSU2689||GSU2689||hypothetical protein (VIMSS)||113, 157|
|GSU2791||GSU2791||hypothetical protein (RefSeq)||65, 157|
|GSU3012||GSU3012||hypothetical protein (VIMSS)||38, 157|
|GSU3324||GSU3324||transcriptional regulator, Cro/CI family (VIMSS)||13, 157|
|GSU3345||GSU3345||hypothetical protein (VIMSS)||113, 157|
|GSU3414||GSU3414||hypothetical protein (VIMSS)||41, 157|
|GSU3415||GSU3415||radical SAM domain protein/B12 binding domain protein (NCBI)||21, 157|
|GSU3417||GSU3417||dioxygenase, putative (VIMSS)||21, 59|
|GSU3418||GSU3418||sigma-54 dependent DNA-binding response regulator (VIMSS)||21, 274|
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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