Organism : Geobacter sulfurreducens | Module List :
Regulation information for GSU2671(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 GSU2671
|Gene||Common Name||Description||Module membership|
|GSU0120||GSU0120||hydrogenase maturation protease (VIMSS)||82, 141|
|GSU0217||noxC||nitroreductase family protein (NCBI)||110, 304|
|GSU0264||GSU0264||drug resistance transporter, Bcr/CflA family (VIMSS)||82, 141|
|GSU0275||GSU0275||hypothetical protein (VIMSS)||82, 141|
|GSU0277||GSU0277||ABC transporter, ATP-binding/permease protein (VIMSS)||104, 304|
|GSU0278||GSU0278||outer membrane efflux protein (VIMSS)||82, 141|
|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|
|GSU0400||GSU0400||methyl-accepting chemotaxis protein (VIMSS)||82, 156|
|GSU0425||fliR||flagellar biosynthesis protein FliR (NCBI)||82, 141|
|GSU0426||flhB||flagellar biosynthetic protein FlhB (NCBI)||82, 275|
|GSU0698||GSU0698||PBS lyase HEAT-like repeat protein (NCBI)||296, 304|
|GSU0766||GSU0766||methyl-accepting chemotaxis protein, putative (VIMSS)||82, 272|
|GSU0899||GSU0899||conserved hypothetical protein (VIMSS)||69, 304|
|GSU0920||GSU0920||hypothetical protein (NCBI)||82, 296|
|GSU0935||GSU0935||methyl-accepting chemotaxis protein, putative (VIMSS)||155, 304|
|GSU0943||GSU0943||hypothetical protein (VIMSS)||304, 335|
|GSU0951||GSU0951||transcriptional regulator, TetR family (VIMSS)||82, 296|
|GSU1097||pstA||phosphate ABC transporter, permease protein (NCBI)||82, 141|
|GSU1169||GSU1169||hypothetical protein (VIMSS)||165, 304|
|GSU1294||GSU1294||methyl-accepting chemotaxis protein (VIMSS)||82, 190|
|GSU1304||GSU1304||methyl-accepting chemotaxis protein (VIMSS)||82, 155|
|GSU1315||merA-1||mercuric reductase (NCBI)||296, 304|
|GSU1372||GSU1372||3-hydroxyisobutyrate dehydrogenase family protein (VIMSS)||59, 304|
|GSU1550||GSU1550||4-oxalocrotonate tautomerase family protein (VIMSS)||220, 304|
|GSU1619||cheY-4||chemotaxis protein CheY (NCBI)||59, 304|
|GSU1713||GSU1713||conserved hyothetical protein, truncation (VIMSS)||70, 304|
|GSU2160||GSU2160||hypothetical protein (VIMSS)||78, 82|
|GSU2186||GSU2186||conserved hypothetical protein (VIMSS)||82, 190|
|GSU2187||GSU2187||ABC transporter, permease protein (VIMSS)||82, 190|
|GSU2188||GSU2188||ABC transporter, ATP-binding protein (VIMSS)||82, 190|
|GSU2189||GSU2189||sensor histidine kinase (VIMSS)||82, 190|
|GSU2299||GSU2299||cytochrome c family protein (NCBI)||82, 141|
|GSU2385||GSU2385||hypothetical protein (VIMSS)||82, 278|
|GSU2388||GSU2388||sensory box histidine kinase (VIMSS)||82, 155|
|GSU2401||GSU2401||sensory box histidine kinase/response regulator (VIMSS)||82, 141|
|GSU2531||GSU2531||sensory box histidine kinase (VIMSS)||79, 82|
|GSU2535||GSU2535||response regulator (VIMSS)||82, 224|
|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|
|GSU2580||GSU2580||hypothetical protein (VIMSS)||82, 141|
|GSU2646||GSU2646||hypothetical protein (VIMSS)||79, 304|
|GSU2671||GSU2671||hypothetical protein (VIMSS)||82, 304|
|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|
|GSU3104||prfA||peptide chain release factor 1 (NCBI)||82, 140|
|GSU3154||GSU3154||cytochrome c nitrite reductase, catalytic subunit NrfA, putative (VIMSS)||16, 82|
|GSU3155||GSU3155||cytochrome c nitrite reductase, small subunit NrfH, putative (VIMSS)||78, 304|
|GSU3221||GSU3221||cytochrome c family protein (NCBI)||6, 82|
|GSU3227||GSU3227||hypothetical protein (VIMSS)||82, 141|
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.
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.
- 2. Source gene
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