Organism : Halobacterium salinarum NRC-1 | Module List :
Regulation information for VNG6348H(Mouseover regulator name to see its description)
Motif information (de novo identified motifs for modules)
There are 10 motifs predicted.
|Motif Id||e-value||Consensus||Motif Logo|
Module neighborhood information for VNG6348H
|Gene||Common Name||Description||Module membership|
|VNG0062G||lpb||LPS biosynthesis protein||106, 164|
|VNG0117H||hypothetical protein VNG0117H||72, 207, 209, 243, 298|
|VNG0138H||hypothetical protein VNG0138H||57, 209, 298|
|VNG0187H||hypothetical protein VNG0187H||160|
|VNG0243Cm||truD||tRNA pseudouridine synthase D||86, 130, 209, 298|
|VNG0318G||dpg||dolichol-P-glucose synthetase||118, 160, 232, 243|
|VNG0499G||cna||proliferating-cell nucleolar antigen||57, 86, 139, 209, 298|
|VNG0595H||hypothetical protein VNG0595H||139, 209, 298|
|VNG0622H||hypothetical protein VNG0622H||139, 209, 298|
|VNG0664G||birL||biotin acetyl-CoA carboxylase ligase||160|
|VNG0725H||hypothetical protein VNG0725H||160|
|VNG0818C||hypothetical protein VNG0818C||86, 106, 243, 298|
|VNG0851C||hypothetical protein VNG0851C||160, 284|
|VNG0938G||gufA||GufA protein||57, 86, 139, 209, 298|
|VNG1287C||hypothetical protein VNG1287C||131, 160|
|VNG1394H||hypothetical protein VNG1394H||86, 209, 214, 298|
|VNG1455H||hypothetical protein VNG1455H||26, 31, 57, 86|
|VNG1574G||cobI||cobalamin adenosyltransferase||86, 210|
|VNG1589C||hypothetical protein VNG1589C||4, 5, 8, 28, 69, 85, 204|
|VNG1785G||panF||hypothetical protein VNG1785G||57, 86, 232, 243, 298|
|VNG1788C||hypothetical protein VNG1788C||186, 209|
|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|
|VNG1917H||hypothetical protein VNG1917H||139, 209, 298|
|VNG2087G||hisH||imidazole glycerol phosphate synthase subunit HisH||86, 106, 209, 298|
|VNG2156C||hypothetical protein VNG2156C||57, 106, 209, 243, 298|
|VNG2270G||mutS3||hypothetical protein VNG2270G||57, 86, 298|
|VNG2335H||hypothetical protein VNG2335H||57, 86, 106, 139, 209, 257, 298|
|VNG6143H||hypothetical protein VNG6143H||5, 26, 31, 72, 86, 106, 204, 232, 243, 295, 298|
|VNG6145H||hypothetical protein VNG6145H||31, 72, 86, 106, 232, 298|
|VNG6165H||hypothetical protein VNG6165H||85|
|VNG6170H||hypothetical protein VNG6170H||4, 5, 15, 26, 28, 31, 36, 53, 60, 63, 69, 72, 85, 122|
|VNG6171H||hypothetical protein VNG6171H||85|
|VNG6173C||hypothetical protein VNG6173C||85|
|VNG6288C||hypothetical protein VNG6288C||209|
|VNG6335H||hypothetical protein VNG6335H||106, 204|
|VNG6339H||hypothetical protein VNG6339H||26, 31, 69, 86, 106, 204, 232|
|VNG6343H||hypothetical protein VNG6343H||47, 69, 85|
|VNG6348H||hypothetical protein VNG6348H||85, 86, 106, 160, 209|
|VNG6364H||hypothetical protein VNG6364H||31, 106|
|VNG6365H||hypothetical protein VNG6365H||86, 209|
|VNG6384H||hypothetical protein VNG6384H||20, 131, 160, 232|
|VNG6409H||hypothetical protein VNG6409H||85, 152, 153, 158, 160, 198, 203|
|VNG6432H||hypothetical protein VNG6432H||17, 26, 31, 38, 106, 243|
|VNG7047||hypothetical protein VNG7047||57, 86, 209, 216, 298|
|VNG7056||hypothetical protein VNG7056||86, 105, 106, 186, 209, 232, 238, 243, 257, 298|
|VNG7097||hypothetical protein VNG7097||56, 160|
|VNG7099||hypothetical protein VNG7099||57, 209|
|VNG7117||hypothetical protein VNG7117||86, 106|
|VNG7127||hypothetical protein VNG7127||86, 106, 209, 257, 298|
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.
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".
For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.
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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- 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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