Organism : Desulfovibrio vulgaris Hildenborough | Module List :
hypothetical protein DVU1210
Functional Annotations (1)
|Predicted metal-binding, possibly nucleic acid-binding protein||cog/ cog|
Regulation information for DVU1210(Mouseover regulator name to see its description)
Motif information (de novo identified motifs for modules)
There are 4 motifs predicted.
Click on the RegPredict links to explore the motif in RegPredict.
|Motif Id||e-value||Consensus||Motif Logo||RegPredict|
Functional Enrichment for DVU1210
|Predicted metal-binding, possibly nucleic acid-binding protein||cog/ cog|
Module neighborhood information for DVU1210
|Gene||Common Name||Description||Module membership|
|DVU0703||lepA||GTP-binding protein LepA||28, 65|
|DVU0757||hypothetical protein DVU0757||28, 211|
|DVU0786||penicillin-binding protein||28, 270|
|DVU0807||trmU||tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase||15, 28|
|DVU0808||gatA||aspartyl/glutamyl-tRNA amidotransferase subunit A||28, 278|
|DVU0840||ffh||signal recognition particle protein||28, 188|
|DVU0867||aromatic amino acid decarboxylase||28, 306|
|DVU0868||cdsA||phosphatidate cytidylyltransferase||28, 65|
|DVU0869||uppS||undecaprenyl diphosphate synthase||28, 278|
|DVU0871||pyrH||uridylate kinase||28, 65|
|DVU0906||lipB||lipoate-protein ligase B||28, 32|
|DVU1002||hypothetical protein DVU1002||169, 172|
|DVU1003||dnaJ domain-containing protein||169, 172|
|DVU1044||guaB||inosine-5`-monophosphate dehydrogenase||28, 270|
|DVU1194||hypothetical protein DVU1194||169, 308|
|DVU1196||leuS||leucyl-tRNA synthetase||65, 169|
|DVU1198||ribH||6,7-dimethyl-8-ribityllumazine synthase||169, 248|
|DVU1200||ribE||riboflavin synthase subunit alpha||169, 308|
|DVU1201||ribD||riboflavin biosynthesis protein RibD||94, 169|
|DVU1202||cytidine/deoxycytidylate deaminase family protein||10, 169|
|DVU1203||glyA||serine hydroxymethyltransferase||169, 248|
|DVU1204||fabF||3-oxoacyl-ACP synthase||169, 248|
|DVU1205||acpP||acyl carrier protein||169, 323|
|DVU1206||fabG||3-oxoacyl-ACP reductase||169, 323|
|DVU1207||fabH||3-oxoacyl-ACP synthase||10, 169|
|DVU1208||plsX||glycerol-3-phosphate acyltransferase PlsX||28, 124|
|DVU1209||rpmF||50S ribosomal protein L32||169, 308|
|DVU1210||hypothetical protein DVU1210||28, 169|
|DVU1211||rpmB||50S ribosomal protein L28||169, 308|
|DVU1240||hypothetical protein DVU1240||28, 270|
|DVU1247||hypothetical protein DVU1247||28, 235|
|DVU1538||hypothetical protein DVU1538||28, 278|
|DVU1621||hypothetical protein DVU1621||28, 65|
|DVU1780||hypothetical protein DVU1780||169, 229|
|DVU1781||hypothetical protein DVU1781||169, 229|
|DVU1782||iron-sulfur cluster-binding protein||169, 229|
|DVU1783||hypothetical protein DVU1783||169, 229|
|DVU1784||short chain dehydrogenase/reductase family oxidoreductase||169, 229|
|DVU1785||MarC membrane protein||169, 229|
|DVU1788||rpoD||RNA polymerase sigma-70 factor||28, 227|
|DVU1789||dnaG||DNA primase||28, 227|
|DVU1790||MutS2 family protein||1, 28|
|DVU1791||GatB/Yqey family protein||28, 94|
|DVU1890||hemC||porphobilinogen deaminase||28, 270|
|DVU1891||hypothetical protein DVU1891||27, 169|
|DVU1897||glyS||glycyl-tRNA synthetase subunit beta||28, 270|
|DVU1898||glyQ||glycyl-tRNA synthetase subunit alpha||28, 270|
|DVU1949||nifA-1||nif-specific regulatory protein||28, 270|
|DVU1951||indolepyruvate ferredoxin oxidoreductase subunit alpha||28, 270|
|DVU1952||hypothetical protein DVU1952||28, 113|
|DVU2343||amino acid ABC transporter ATP-binding protein||3, 28|
|DVU3176||UDP-glucose/GDP-mannose dehydrogenase family protein||169, 292|
|DVU3177||hypothetical protein DVU3177||145, 169|
|DVU3243||dnaJ||chaperone protein DnaJ||28, 227|
|DVU3365||fmt||methionyl-tRNA formyltransferase||28, 227|
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.
You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".
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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.
Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.
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.
- 2. Source gene
- 3. Target genes (other module members)
- 4. Interactions between source and target genes for a particular module
- 5. Module(s) that source gene and target genes belong to
- 6. Visualisation legend
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