Organism : Halobacterium salinarum NRC-1 | Module List :
Regulation information for VNG1811G(Mouseover regulator name to see its description)
Motif information (de novo identified motifs for modules)
There are 8 motifs predicted.
|Motif Id||e-value||Consensus||Motif Logo|
Functional Enrichment for VNG1811G
Module neighborhood information for VNG1811G
|Gene||Common Name||Description||Module membership|
|VNG0316C||hypothetical protein VNG0316C||42, 68|
|VNG0430H||hypothetical protein VNG0430H||42, 68, 151|
|VNG0462C||hypothetical protein VNG0462C||42, 57, 68, 151, 162, 246|
|VNG0819C||hypothetical protein VNG0819C||42|
|VNG0836H||hypothetical protein VNG0836H||42, 68|
|VNG0858C||hypothetical protein VNG0858C||68|
|VNG0870G||gatC||hypothetical protein VNG0870G||42, 68|
|VNG0988H||hypothetical protein VNG0988H||42, 68, 107, 203, 207, 210|
|VNG1112H||hypothetical protein VNG1112H||173, 179, 280|
|VNG1204G||gdhA2||hypothetical protein VNG1204G||88, 154, 179|
|VNG1205C||N-ethylammeline chlorohydrolase||179, 285|
|VNG1270H||hypothetical protein VNG1270H||18, 30, 37, 42|
|VNG1362H||hypothetical protein VNG1362H||68|
|VNG1784C||DNA primase||28, 42, 68, 83, 234|
|VNG1811G||eye||succinoglycan biosynthesis||42, 68, 179, 286|
|VNG1814G||carB||carbamoyl phosphate synthase large subunit||179|
|VNG1815G||carA||carbamoyl phosphate synthase small subunit||68, 86, 209, 257, 294, 298|
|VNG1816G||trh3||transcription regulator||68, 86, 139, 209, 238, 257, 298|
|VNG1818G||idi||Idi||68, 86, 209, 214, 234, 257|
|VNG1859G||deoC||hypothetical protein VNG1859G||42, 68|
|VNG1872C||hypothetical protein VNG1872C||42, 68, 186|
|VNG1886C||hypothetical protein VNG1886C||42, 68|
|VNG1891H||hypothetical protein VNG1891H||14, 42, 68, 135|
|VNG1893G||trp2||ABC transport protein||14, 42|
|VNG1894C||hypothetical protein VNG1894C||14, 42|
|VNG1921H||hypothetical protein VNG1921H||68|
|VNG1952H||hypothetical protein VNG1952H||18, 28, 30, 42, 68, 80, 91, 108, 121, 135|
|VNG1953C||hypothetical protein VNG1953C||13, 18, 30, 34, 42, 80, 91, 108, 115, 121|
|VNG1956H||hypothetical protein VNG1956H||18, 30, 34, 42, 80, 91, 108, 115, 121|
|VNG1974H||hypothetical protein VNG1974H||118, 286|
|VNG1980C||hypothetical protein VNG1980C||68, 135|
|VNG2011G||thiL||hypothetical protein VNG2011G||88, 179, 206|
|VNG2246H||hypothetical protein VNG2246H||286|
|VNG2298H||hypothetical protein VNG2298H||42, 68, 152|
|VNG2501C||hypothetical protein VNG2501C||68, 214, 234|
|VNG2570G||dcd||deoxyuridine 5'-triphosphate nucleotidohydrolase||129, 179|
|VNG2669G||cyo||cytochrome oxidase subunit I-like protein||44, 179|
|VNG5175H||None||42, 68, 234|
|VNG6142C||hypothetical protein VNG6142C||42, 68, 295|
|VNG6144G||trsE||transfer complex protein||4, 5, 42, 68, 295|
|VNG6148H||hypothetical protein VNG6148H||42, 68|
|VNG6158H||hypothetical protein VNG6158H||42, 68|
|VNG6168H||hypothetical protein VNG6168H||38, 42|
|VNG6187G||orc3||orc / cell division control protein 6||42, 68|
|VNG6189H||hypothetical protein VNG6189H||118, 286|
|VNG6193H||hypothetical protein VNG6193H||17, 32, 34, 38, 41, 42, 44, 80|
|VNG6203H||hypothetical protein VNG6203H||42|
|VNG6232G||gvpJ2||GvpJ protein, cluster B||4, 5, 8, 28, 31, 42, 141, 148, 182, 188|
|VNG6235G||gvpH2||GvpH protein, cluster B||31, 42, 141, 188|
|VNG6242G||gvpC2||GvpC protein, cluster B||42, 185|
|VNG6269C||hypothetical protein VNG6269C||179|
|VNG7033||hypothetical protein VNG7033||97, 179|
|VNG7034||hypothetical protein VNG7034||97, 179|
|VNG7123||arsA||arsenical resistance ATPase A||217, 286|
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.
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.
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.
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