Organism : Geobacter sulfurreducens | Module List :
glutaredoxin family protein (VIMSS)
Functional Annotations (5)
|Glutaredoxin and related proteins||cog/ cog|
|electron carrier activity||go/ molecular_function|
|protein disulfide oxidoreductase activity||go/ molecular_function|
|cell redox homeostasis||go/ biological_process|
Regulation information for GSU1155(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 GSU1155
Module neighborhood information for GSU1155
|Gene||Common Name||Description||Module membership|
|GSU0276||GSU0276||secretion protein, HlyD family (VIMSS)||217, 293|
|GSU0369||GSU0369||FlhB domain protein, putative (NCBI)||293, 300|
|GSU0462||GSU0462||peptidase, M48 family (NCBI)||51, 63|
|GSU0463||GSU0463||membrane protein, putative (VIMSS)||36, 51|
|GSU0702||GSU0702||cytochrome c family protein (VIMSS)||51, 76|
|GSU0748||GSU0748||hypothetical protein (VIMSS)||217, 293|
|GSU0877||GSU0877||response regulator (VIMSS)||51, 76|
|GSU0947||GSU0947||ABC transporter, ATP-binding protein (VIMSS)||272, 293|
|GSU0993||GSU0993||conserved hypothetical protein (VIMSS)||283, 293|
|GSU1155||GSU1155||glutaredoxin family protein (VIMSS)||51, 293|
|GSU1202||rfbA||mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase, truncation (NCBI)||51, 144|
|GSU1285||GSU1285||sensory box sensor histidine kinase/response regulator (VIMSS)||63, 293|
|GSU1295||GSU1295||conserved hypothetical protein (VIMSS)||266, 293|
|GSU1296||GSU1296||sensory box histidine kinase/response regulator (VIMSS)||293, 337|
|GSU1359||GSU1359||helicase, putative (NCBI)||232, 293|
|GSU1406||GSU1406||conserved domain protein (VIMSS)||163, 293|
|GSU1491||GSU1491||type IV pilus biogenesis protein PilB (VIMSS)||51, 75|
|GSU1564||GSU1564||Glu/Leu/Phe/Val dehydrogenase family protein (NCBI)||51, 76|
|GSU1572||GSU1572||ribD domain protein (NCBI)||51, 79|
|GSU1643||pleD||GGDEF/response regulator receiver domain protein (NCBI)||51, 293|
|GSU1678||GSU1678||cation-transport ATPase, E1-E2 family (VIMSS)||293, 318|
|GSU1679||GSU1679||hypothetical protein (VIMSS)||51, 249|
|GSU1715||GSU1715||hypothetical protein (VIMSS)||51, 181|
|GSU1742||GSU1742||Na/Pi-cotransporter family protein (VIMSS)||287, 293|
|GSU1818||GSU1818||phosphoglycerate mutase family protein (NCBI)||163, 293|
|GSU1819||xerD||integrase/recombinase XerD (NCBI)||163, 293|
|GSU2131||GSU2131||hypothetical protein (VIMSS)||51, 66|
|GSU2194||guaA||GMP synthase (NCBI)||51, 201|
|GSU2216||GSU2216||PBS lyase HEAT-like repeat protein (NCBI)||51, 293|
|GSU2224||GSU2224||response regulator (VIMSS)||51, 201|
|GSU2377||GSU2377||hypothetical protein (VIMSS)||51, 158|
|GSU2420||GSU2420||ferredoxin family protein (VIMSS)||57, 293|
|GSU2422||GSU2422||hydrogenase maturation protease (VIMSS)||283, 293|
|GSU2450||GSU2450||conserved hypothetical protein (VIMSS)||51, 59|
|GSU2453||GSU2453||membrane protein, putative (VIMSS)||51, 79|
|GSU2554||GSU2554||conserved hypothetical protein (VIMSS)||51, 231|
|GSU2773||GSU2773||conserved domain protein (VIMSS)||51, 179|
|GSU2995||cobI||precorrin-2 C20-methyltransferase (NCBI)||51, 76|
|GSU3159||GSU3159||MutT/nudix family protein (VIMSS)||293, 318|
|GSU3171||GSU3171||conserved domain protein (NCBI)||51, 103|
|GSU3181||GSU3181||Beta-ketoacyl synthase domain protein (VIMSS)||163, 293|
|GSU3250||pcnB||polyA polymerase (NCBI)||51, 73|
|GSU3309||GSU3309||conserved hypothetical protein (VIMSS)||51, 121|
|GSU3354||GSU3354||MutT/nudix family protein (VIMSS)||226, 293|
|GSU3362||GSU3362||hypothetical protein (VIMSS)||232, 293|
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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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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