Organism : Geobacter sulfurreducens | Module List :
phosphate transport system regulatory protein PhoU (NCBI)
Functional Annotations (2)
|Phosphate uptake regulator||cog/ cog|
Regulation information for GSU1095(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 GSU1095
|Phosphate uptake regulator||cog/ cog|
Module neighborhood information for GSU1095
|Gene||Common Name||Description||Module membership|
|GSU0123||GSU0123||nickel-dependent hydrogenase, small subunit (VIMSS)||96, 252|
|GSU0373||GSU0373||sensor histidine kinase (VIMSS)||96, 220|
|GSU0396||GSU0396||conserved hypothetical protein (VIMSS)||96, 229|
|GSU0427||GSU0427||lipoprotein, putative (VIMSS)||96, 278|
|GSU0431||GSU0431||conserved hypothetical protein (VIMSS)||96, 130|
|GSU0432||GSU0432||conserved hypothetical protein (VIMSS)||96, 278|
|GSU0433||GSU0433||clpB protein, putative (NCBI)||21, 96|
|GSU0449||GSU0449||hypothetical protein (VIMSS)||96, 137|
|GSU0574||GSU0574||membrane protein, putative (VIMSS)||96, 186|
|GSU0801||GSU0801||hypothetical protein (VIMSS)||96, 109|
|GSU1032||GSU1032||methyl-accepting chemotaxis protein (VIMSS)||1, 337|
|GSU1037||GSU1037||sensory box/response regulator (VIMSS)||1, 224|
|GSU1095||phoU||phosphate transport system regulatory protein PhoU (NCBI)||1, 96|
|GSU1146||GSU1146||conserved domain protein (NCBI)||96, 109|
|GSU1407||GSU1407||hypothetical protein (VIMSS)||1, 268|
|GSU1676||GSU1676||hypothetical protein (VIMSS)||96, 236|
|GSU1988||GSU1988||hypothetical protein (VIMSS)||96, 206|
|GSU2094||GSU2094||response regulator (VIMSS)||1, 287|
|GSU2095||GSU2095||NADH oxidase, putative (VIMSS)||1, 79|
|GSU2098||cooS||carbon monoxide dehydrogenase subunit (NCBI)||1, 178|
|GSU2115||GSU2115||hypothetical protein (VIMSS)||1, 16|
|GSU2152||GSU2152||hypothetical protein (VIMSS)||1, 213|
|GSU2154||GSU2154||hypothetical protein (VIMSS)||1, 337|
|GSU2156||GSU2156||hypothetical protein (VIMSS)||1, 70|
|GSU2158||norQ||cobS protein, putative (NCBI)||1, 322|
|GSU2162||GSU2162||hypothetical protein (VIMSS)||1, 224|
|GSU2165||GSU2165||hypothetical protein (VIMSS)||1, 78|
|GSU2166||GSU2166||hypothetical protein (VIMSS)||1, 300|
|GSU2167||GSU2167||CHC2 zinc finger domain protein (VIMSS)||1, 78|
|GSU2168||radC||DNA repair protein RadC (NCBI)||1, 163|
|GSU2169||GSU2169||hypothetical protein (VIMSS)||96, 174|
|GSU2309||GSU2309||metallo-beta-lactamase family protein (VIMSS)||96, 130|
|GSU2372||GSU2372||methyl-accepting chemotaxis protein, putative (VIMSS)||96, 220|
|GSU2421||GSU2421||hypothetical protein (VIMSS)||1, 190|
|GSU2480||kdpA||potassium-transporting ATPase, A subunit (NCBI)||96, 252|
|GSU2481||kdpB||potassium-transporting ATPase, B subunit (NCBI)||96, 257|
|GSU2484||kdpE||DNA-binding response regulator KdpE (NCBI)||96, 257|
|GSU2534||GSU2534||sensory box/response regulator (VIMSS)||96, 266|
|GSU2661||GSU2661||conserved hypothetical protein (VIMSS)||1, 287|
|GSU2776||GSU2776||conserved hypothetical protein (NCBI)||1, 9|
|GSU2984||znuC||permease component of zinc ABC transporter (Dmitry Rodionov)||96, 287|
|GSU3019||GSU3019||dehydrogenase, E1 component, alpha and beta subunits (NCBI)||27, 96|
|GSU3121||GSU3121||EF hand domain protein (VIMSS)||1, 224|
|GSU3180||GSU3180||conserved hypothetical protein (VIMSS)||1, 180|
|GSU3239||cafA||ribonuclease G (NCBI)||96, 236|
|GSU3400||GSU3400||heavy metal efflux pump, CzcA family (VIMSS)||1, 337|
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.
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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- 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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