Organism : Geobacter sulfurreducens | Module List :
RNA pseudouridine synthase family protein (NCBI)
Functional Annotations (4)
|Pseudouridylate synthases, 23S RNA-specific||cog/ cog|
|pseudouridine synthesis||go/ biological_process|
|RNA binding||go/ molecular_function|
|pseudouridine synthase activity||go/ molecular_function|
Regulation information for GSU3353(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 GSU3353
Module neighborhood information for GSU3353
|Gene||Common Name||Description||Module membership|
|GSU0007||GSU0007||sensory box histidine kinase (VIMSS)||147, 159|
|GSU0107||spo0J||parB-like domain protein (NCBI)||147, 181|
|GSU0154||GSU0154||mutT/nudix family protein (NCBI)||112, 289|
|GSU0155||GSU0155||hypothetical protein (VIMSS)||160, 289|
|GSU0156||argH||argininosuccinate lyase (NCBI)||222, 289|
|GSU0205||GSU0205||transcriptional regulator, TetR family (VIMSS)||112, 289|
|GSU0272||GSU0272||hypothetical protein (VIMSS)||285, 289|
|GSU0446||GSU0446||conserved hypothetical protein TIGR00046 (VIMSS)||147, 183|
|GSU0483||GSU0483||exsB protein (VIMSS)||112, 289|
|GSU0606||alr||alanine racemase (NCBI)||147, 231|
|GSU0607||selD||selenide, water dikinase, selenocysteine-containing (NCBI)||147, 231|
|GSU0679||GSU0679||tellurite resistance protein-related protein (VIMSS)||25, 147|
|GSU0689||GSU0689||protein export membrane protein, SecD/SecF family, putative (VIMSS)||147, 309|
|GSU0751||GSU0751||conserved hypothetical protein (VIMSS)||147, 183|
|GSU0793||GSU0793||hypothetical protein (VIMSS)||202, 289|
|GSU0847||GSU0847||rubredoxin (VIMSS)||208, 289|
|GSU0850||GSU0850||hypothetical protein (NCBI)||258, 289|
|GSU0932||uraA||uracil permease (NCBI)||147, 164|
|GSU1227||GSU1227||ABC transporter, ATP-binding protein (VIMSS)||11, 147|
|GSU1228||GSU1228||cytochrome c family protein (VIMSS)||11, 147|
|GSU1291||GSU1291||response regulator (VIMSS)||147, 158|
|GSU1527||GSU1527||conserved hypothetical protein (VIMSS)||147, 183|
|GSU1541||GSU1541||conserved hypothetical protein (VIMSS)||13, 147|
|GSU1543||GSU1543||hypothetical protein (VIMSS)||147, 262|
|GSU1832||GSU1832||conserved hypothetical protein (NCBI)||112, 289|
|GSU1838||hrpB||ATP-dependent helicase HrpB (NCBI)||147, 338|
|GSU1917||uppS||undecaprenyl diphosphate synthase (NCBI)||147, 333|
|GSU2078||rodA||rod shape-determining protein RodA (NCBI)||147, 207|
|GSU2200||GSU2200||hypothetical protein (VIMSS)||40, 289|
|GSU2283||GSU2283||diacylglycerol kinase, putative (NCBI)||207, 289|
|GSU2334||GSU2334||hypothetical protein (VIMSS)||59, 147|
|GSU2339||GSU2339||monovalent cation/proton antiporter, MrpF/PhaF family (NCBI)||94, 289|
|GSU2341||GSU2341||NADH-ubiquinone/plastoquinone family protein (VIMSS)||40, 289|
|GSU2545||maf||maf protein (NCBI)||42, 147|
|GSU2552||GSU2552||lipoprotein, putative (VIMSS)||231, 289|
|GSU2647||GSU2647||conserved hypothetical protein (VIMSS)||11, 147|
|GSU2694||GSU2694||hypothetical protein (VIMSS)||17, 147|
|GSU2718||hoxH||NAD-reducing hydrogenase, beta subunit (NCBI)||40, 289|
|GSU2727||GSU2727||hypothetical protein (VIMSS)||11, 147|
|GSU2756||GSU2756||hypothetical protein (VIMSS)||147, 176|
|GSU2783||GSU2783||HDIG domain protein (VIMSS)||147, 296|
|GSU2990||cobD||cobalamin biosynthesis protein CobD (NCBI)||112, 289|
|GSU3205||GSU3205||MiaB-like tRNA modifying enzyme YliG (NCBI)||47, 147|
|GSU3307||hisS||histidyl-tRNA synthetase, putative (NCBI)||147, 245|
|GSU3353||rluD||RNA pseudouridine synthase family protein (NCBI)||147, 289|
|GSU3383||gatC||glutamyl-tRNA(Gln) amidotransferase, C subunit (NCBI)||112, 289|
|GSU3457||GSU3457||glycine cleavage system transcriptional repressor, putative (VIMSS)||112, 289|
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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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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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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