Organism : Geobacter sulfurreducens | Module List :
Regulation information for GSU0943(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 GSU0943
|Gene||Common Name||Description||Module membership|
|GSU0102||selB||selenocysteine-specific translation elongation factor (NCBI)||335, 338|
|GSU0106||GSU0106||soj protein (VIMSS)||286, 335|
|GSU0115||pdxA||pyridoxal phosphate biosynthetic protein PdxA (NCBI)||200, 335|
|GSU0176||GSU0176||conserved hypothetical protein (VIMSS)||173, 335|
|GSU0217||noxC||nitroreductase family protein (NCBI)||110, 304|
|GSU0277||GSU0277||ABC transporter, ATP-binding/permease protein (VIMSS)||104, 304|
|GSU0294||GSU0294||HD domain protein (NCBI)||220, 304|
|GSU0372||GSU0372||sigma-54 dependent DNA-binding response regulator (VIMSS)||224, 304|
|GSU0374||hypA||hydrogenase expression/formation protein hupa (NCBI)||283, 304|
|GSU0375||gcvT||glycine cleavage system T protein (NCBI)||296, 304|
|GSU0551||GSU0551||conserved hypothetical protein (VIMSS)||173, 335|
|GSU0560||GSU0560||hypothetical protein (VIMSS)||179, 335|
|GSU0698||GSU0698||PBS lyase HEAT-like repeat protein (NCBI)||296, 304|
|GSU0887||GSU0887||conserved hypothetical protein (VIMSS)||144, 335|
|GSU0899||GSU0899||conserved hypothetical protein (VIMSS)||69, 304|
|GSU0935||GSU0935||methyl-accepting chemotaxis protein, putative (VIMSS)||155, 304|
|GSU0943||GSU0943||hypothetical protein (VIMSS)||304, 335|
|GSU1006||GSU1006||hypothetical protein (VIMSS)||265, 335|
|GSU1169||GSU1169||hypothetical protein (VIMSS)||165, 304|
|GSU1191||GSU1191||hypothetical protein (VIMSS)||335, 338|
|GSU1315||merA-1||mercuric reductase (NCBI)||296, 304|
|GSU1355||GSU1355||ISGsu7, transposase OrfA (VIMSS)||335, 341|
|GSU1356||GSU1356||ISGsu7, transposase OrfB (VIMSS)||47, 335|
|GSU1372||GSU1372||3-hydroxyisobutyrate dehydrogenase family protein (VIMSS)||59, 304|
|GSU1475||GSU1475||RNA methyltransferase, TrmH family, group 1 (VIMSS)||124, 335|
|GSU1550||GSU1550||4-oxalocrotonate tautomerase family protein (VIMSS)||220, 304|
|GSU1609||GSU1609||outer membrane efflux protein (VIMSS)||159, 335|
|GSU1619||cheY-4||chemotaxis protein CheY (NCBI)||59, 304|
|GSU1713||GSU1713||conserved hyothetical protein, truncation (VIMSS)||70, 304|
|GSU1820||GSU1820||protein-P-II uridylyltransferase, putative (VIMSS)||163, 335|
|GSU1870||GSU1870||GGDEF domain protein (VIMSS)||183, 335|
|GSU1940||GSU1940||sigma-54 dependent DNA-binding response regulator (VIMSS)||158, 335|
|GSU1941||GSU1941||sensor histidine kinase (VIMSS)||159, 335|
|GSU2455||GSU2455||conserved hypothetical protein (VIMSS)||163, 335|
|GSU2538||nspC||carboxynorspermidine decarboxylase (NCBI)||15, 304|
|GSU2539||LYS1||saccharopine dehydrogenase (NCBI)||25, 304|
|GSU2540||GSU2540||transcriptional regulator, Cro/CI family (VIMSS)||181, 304|
|GSU2541||proC||pyrroline-5-carboxylate reductase (NCBI)||114, 304|
|GSU2577||GSU2577||hypothetical protein (VIMSS)||296, 304|
|GSU2646||GSU2646||hypothetical protein (VIMSS)||79, 304|
|GSU2671||GSU2671||hypothetical protein (VIMSS)||82, 304|
|GSU2710||GSU2710||hypothetical protein (NCBI)||140, 335|
|GSU2717||GSU2717||conserved hypothetical protein (VIMSS)||144, 335|
|GSU2744||GSU2744||major facilitator family transporter (VIMSS)||49, 304|
|GSU2745||GSU2745||ATPase, AAA family (VIMSS)||49, 304|
|GSU2746||GSU2746||conserved domain protein (NCBI)||269, 304|
|GSU3108||rho||transcription termination factor Rho (NCBI)||183, 335|
|GSU3155||GSU3155||cytochrome c nitrite reductase, small subunit NrfH, putative (VIMSS)||78, 304|
|GSU3209||GSU3209||iojap-related protein (VIMSS)||160, 335|
|GSU3282||GSU3282||siroheme synthase, N-terminal domain protein (NCBI)||260, 335|
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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If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.
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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.
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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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