Organism : Halobacterium salinarum NRC-1 | Module List :
hypothetical protein VNG2310H
Functional Annotations (5)
|Glutaredoxin and related proteins||cog/ cog|
|electron transport||go/ biological_process|
|electron carrier activity||go/ molecular_function|
|protein disulfide oxidoreductase activity||go/ molecular_function|
|cell redox homeostasis||go/ biological_process|
Regulation information for VNG2310H(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 VNG2310H
Module neighborhood information for VNG2310H
|Gene||Common Name||Description||Module membership|
|VNG0227H||hypothetical protein VNG0227H||25, 55|
|VNG0254G||tfbG||transcription initiation factor IIB||3, 12, 25, 50, 55, 113|
|VNG0261H||hypothetical protein VNG0261H||7, 12, 16, 25, 49, 50, 55, 79, 109, 113|
|VNG0262C||hypothetical protein VNG0262C||12, 25, 49, 50, 55, 79, 109, 113|
|VNG0321G||ids||Ids||7, 25, 50, 55|
|VNG0533H||hypothetical protein VNG0533H||25, 50|
|VNG0932C||hypothetical protein VNG0932C||25, 50, 61|
|VNG0940Gm||ACS3||Acetyl-CoA synthetase||7, 19, 24, 25, 29, 49|
|VNG0955G||fapE||flagella-like protein E||7, 16, 25, 50, 100, 291|
|VNG0992H||hypothetical protein VNG0992H||229, 283|
|VNG1085H||hypothetical protein VNG1085H||229, 283|
|VNG1264C||hypothetical protein VNG1264C||9, 25, 55, 84|
|VNG1273G||moaC||putative molybdenum cofactor biosynthesis protein MoaC||25, 81|
|VNG1326H||hypothetical protein VNG1326H||25, 50, 55|
|VNG1446H||hypothetical protein VNG1446H||25, 55|
|VNG1660G||sop1||sensory rhodopsin I||229|
|VNG1663C||hypothetical protein VNG1663C||25, 50|
|VNG1664H||hypothetical protein VNG1664H||25, 50|
|VNG1898C||hypothetical protein VNG1898C||25, 50, 55|
|VNG1933G||ftsZ3||cell division protein||7, 25, 61, 227|
|VNG2176H||hypothetical protein VNG2176H||229|
|VNG2195G||coxB2||cytochrome c oxidase subunit II||25, 50|
|VNG2196G||hcpB||halocyanin-like protein||25, 50|
|VNG2259C||phosphoenolpyruvate carboxylase||25, 50|
|VNG2310H||hypothetical protein VNG2310H||25, 229|
|VNG2311H||hypothetical protein VNG2311H||25, 229|
|VNG2432C||hypothetical protein VNG2432C||25, 50|
|VNG2499G||gcdH||glutaryl-CoA dehydrogenase||7, 24, 25, 50, 61, 78|
|VNG2508C||hypothetical protein VNG2508C||25, 50, 55|
|VNG2603H||hypothetical protein VNG2603H||25, 61|
|VNG2604Gm||THI1||ribulose-1,5-biphosphate synthetase||25, 61|
|VNG2606G||thiD||hypothetical protein VNG2606G||25, 61|
|VNG2644C||hypothetical protein VNG2644C||25, 50|
|VNG6162H||hypothetical protein VNG6162H||228, 229, 238|
|VNG6163H||hypothetical protein VNG6163H||228, 229, 238|
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.
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)
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