Organism : Geobacter sulfurreducens | Module List :
Regulation information for GSU3202(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 GSU3202
Module neighborhood information for GSU3202
|Gene||Common Name||Description||Module membership|
|GSU0062||GSU0062||TraD protein, putative (VIMSS)||189, 319|
|GSU0082||RluD||ribosomal large subunit pseudouridine synthase D (NCBI)||261, 326|
|GSU0150||argB||acetylglutamate kinase (NCBI)||107, 189|
|GSU0206||GSU0206||ZIP zinc transporter family protein (VIMSS)||189, 206|
|GSU0231||GSU0231||hypothetical protein (VIMSS)||189, 224|
|GSU0330||GSU0330||general secretion pathway protein C, putative (NCBI)||173, 189|
|GSU0848||GSU0848||ferredoxin family protein, putative (VIMSS)||21, 189|
|GSU1015||GSU1015||hypothetical protein (VIMSS)||21, 189|
|GSU1035||GSU1035||methyl-accepting chemotaxis protein (NCBI)||57, 189|
|GSU1059||sucD||succinyl-CoA synthase, alpha subunit (NCBI)||100, 326|
|GSU1065||GSU1065||hypothetical protein (VIMSS)||173, 189|
|GSU1085||GSU1085||hypothetical protein (VIMSS)||57, 189|
|GSU1142||cheW-3||purine-binding chemotaxis protein CheW (NCBI)||189, 241|
|GSU1161||GSU1161||efflux transporter, RND family, MFP subunit (NCBI)||310, 326|
|GSU1163||GSU1163||ABC transporter, permease protein (VIMSS)||189, 266|
|GSU1220||GSU1220||response regulator (VIMSS)||189, 336|
|GSU1395||GSU1395||hypothetical protein (VIMSS)||57, 189|
|GSU1577||cobO||cob(I)alamin adenosyltransferase (NCBI)||189, 231|
|GSU1614||GSU1614||CoA-binding protein (VIMSS)||20, 326|
|GSU1942||GSU1942||UDP-glucose/GDP-mannose dehydrogenase family protein (VIMSS)||189, 319|
|GSU2013||GSU2013||phosphoglucomutase/phosphomannomutase family protein (VIMSS)||55, 189|
|GSU2118||GSU2118||integrative genetic element Gsu21, integrase (VIMSS)||189, 307|
|GSU2137||GSU2137||metal ion efflux outer membrane protein family protein, putative (VIMSS)||110, 189|
|GSU2175||GSU2175||trfA-related protein (VIMSS)||71, 189|
|GSU2302||GSU2302||trehalose-phosphatase, putative (VIMSS)||20, 189|
|GSU2386||GSU2386||methylcobamide:CoM methyltransferase-related protein (NCBI)||189, 266|
|GSU2393||GSU2393||ISGsu5, transposase, truncation (VIMSS)||121, 189|
|GSU2719||hoxY||NAD-reducing hydrogenase, delta subunit (NCBI)||189, 224|
|GSU2788||GSU2788||conserved hypothetical protein (NCBI)||128, 326|
|GSU3116||GSU3116||1-acyl-sn-glycerol-3-phosphate acyltransferase, putative (NCBI)||81, 189|
|GSU3130||GSU3130||lipoprotein, putative (VIMSS)||100, 326|
|GSU3138||GSU3138||sensor histidine kinase/response regulator (VIMSS)||100, 326|
|GSU3192||GSU3192||heat shock protein, Hsp20 family (NCBI)||104, 326|
|GSU3194||thiL||thiamine monophosphate kinase (NCBI)||128, 326|
|GSU3195||GSU3195||chemotaxis protein methyltransferase CheR,putative (VIMSS)||104, 326|
|GSU3196||GSU3196||methyl-accepting chemotaxis protein (VIMSS)||246, 326|
|GSU3197||GSU3197||purine-binding chemotaxis protein CheW, putative (VIMSS)||246, 326|
|GSU3198||cheY-7||chemotaxis protein CheY (NCBI)||189, 326|
|GSU3199||cheA-3||chemotaxis protein CheA (NCBI)||246, 326|
|GSU3200||GSU3200||chemotaxis protein, CheC family (NCBI)||100, 326|
|GSU3201||GSU3201||chemotaxis protein CheD, putative (VIMSS)||104, 326|
|GSU3202||GSU3202||hypothetical protein (VIMSS)||189, 326|
|GSU3364||GSU3364||hypothetical protein (VIMSS)||81, 189|
|GSU3428||GSU3428||cytochrome c family protein, putative (NCBI)||189, 318|
|GSU3442||GSU3442||conserved hypothetical protein (VIMSS)||167, 326|
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.
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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- 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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