Organism : Geobacter sulfurreducens | Module List :
Regulation information for GSU1024(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 GSU1024
Module neighborhood information for GSU1024
|Gene||Common Name||Description||Module membership|
|GSU0012||hemG||protoporphyrinogen oxidase (VIMSS)||16, 134|
|GSU0014||dnaJ||phage prohead protease, HK97 family/dnaJ domain protein (NCBI)||16, 134|
|GSU0133||GSU0133||hypothetical protein (VIMSS)||16, 86|
|GSU0177||GSU0177||acetyltransferase, GNAT family (NCBI)||16, 60|
|GSU0191||GSU0191||cold-shock domain family protein (VIMSS)||16, 248|
|GSU0209||GSU0209||hypothetical protein (VIMSS)||16, 109|
|GSU0467||GSU0467||hypothetical protein (VIMSS)||16, 86|
|GSU0491||rhlE-1||ATP-dependent RNA helicase RhlE (NCBI)||16, 25|
|GSU0496||GSU0496||efflux transporter, RND family, MFP subunit (NCBI)||20, 290|
|GSU0550||GSU0550||conserved hypothetical protein (VIMSS)||16, 55|
|GSU0558||GSU0558||hypothetical protein (VIMSS)||16, 174|
|GSU0674||hcP-1||hydroxylamine reductase (RefSeq)||16, 214|
|GSU0731||lpxC||UDP-3-0-acyl N-acetylglucosamine deacetylase (NCBI)||16, 140|
|GSU0733||GSU0733||cell shape-determining protein MreB/Mrl family (VIMSS)||15, 16|
|GSU0767||GSU0767||tia invasion determinant-related protein (VIMSS)||20, 288|
|GSU0771||GSU0771||alcohol dehydrogenase, zinc-containing (VIMSS)||16, 257|
|GSU0773||GSU0773||multidrug resistance protein, putative (VIMSS)||16, 257|
|GSU0852||GSU0852||lipoprotein, putative (VIMSS)||16, 65|
|GSU0919||GSU0919||hypothetical protein (VIMSS)||16, 110|
|GSU0921||rne||ribonuclease, Rne/Rng family protein (NCBI)||20, 99|
|GSU0922||GSU0922||ABC transporter, ATP-binding protein (VIMSS)||20, 283|
|GSU0923||loN-1||ATP-dependent protease La (NCBI)||20, 133|
|GSU0924||GSU0924||ABC transporter, permease protein, putative (VIMSS)||20, 133|
|GSU0926||GSU0926||mce-related protein (NCBI)||20, 95|
|GSU0927||GSU0927||peptidase, M16 family (NCBI)||20, 121|
|GSU0928||GSU0928||peptidase, M16 family (NCBI)||20, 57|
|GSU0929||GSU0929||conserved hypothetical protein (VIMSS)||20, 162|
|GSU1017||hpt||hypoxanthine phosphoribosyltransferase, putative (NCBI)||20, 77|
|GSU1024||cyd-4||cytochrome c3 (NCBI)||16, 20|
|GSU1082||GSU1082||conserved hypothetical protein (VIMSS)||16, 77|
|GSU1096||pstB||phosphate ABC transporter, ATP-binding protein (NCBI)||16, 236|
|GSU1394||GSU1394||spore coat protein-related protein (NCBI)||20, 57|
|GSU1401||dnaE||DNA polymerase III, alpha subunit (NCBI)||20, 241|
|GSU1402||accA||acetyl-CoA carboxylase, carboxyl transferase, alpha subunit (NCBI)||20, 321|
|GSU1614||GSU1614||CoA-binding protein (VIMSS)||20, 326|
|GSU1837||GSU1837||peptidase, family M23/M37 domain protein (NCBI)||20, 46|
|GSU1875||ahcY||adenosylhomocysteinase (NCBI)||20, 46|
|GSU2035||GSU2035||hypothetical protein (NCBI)||20, 138|
|GSU2115||GSU2115||hypothetical protein (VIMSS)||1, 16|
|GSU2201||GSU2201||cytochrome c family protein (NCBI)||20, 125|
|GSU2302||GSU2302||trehalose-phosphatase, putative (VIMSS)||20, 189|
|GSU2303||GSU2303||Na+/H+ antiporter family protein (VIMSS)||20, 71|
|GSU2389||GSU2389||ABC transporter, periplasmic substrate-binding protein, putative (NCBI)||16, 55|
|GSU2433||GSU2433||ATP-dependent protease, putative (VIMSS)||20, 49|
|GSU2483||kdpD||sensor histidine kinase KdpD (NCBI)||20, 49|
|GSU2695||GSU2695||outer membrane efflux protein (VIMSS)||16, 86|
|GSU2696||GSU2696||AcrB/AcrD/AcrF family protein (VIMSS)||16, 26|
|GSU2697||GSU2697||multidrug resistance protein (NCBI)||16, 86|
|GSU2883||GSU2883||cytochrome c family protein (VIMSS)||20, 46|
|GSU3091||cvpA||CvpA family protein (NCBI)||16, 236|
|GSU3154||GSU3154||cytochrome c nitrite reductase, catalytic subunit NrfA, putative (VIMSS)||16, 82|
|GSU3156||GSU3156||methyl-accepting chemotaxis protein, putative (VIMSS)||16, 153|
|GSU3225||GSU3225||NHL repeat domain protein (VIMSS)||16, 155|
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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