Organism : Halobacterium salinarum NRC-1 | Module List :
Regulation information for VNG0023H(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 VNG0023H
Module neighborhood information for VNG0023H
|Gene||Common Name||Description||Module membership|
|VNG0014C||hypothetical protein VNG0014C||254, 264|
|VNG0020H||hypothetical protein VNG0020H||30, 108, 247|
|VNG0022H||hypothetical protein VNG0022H||30, 254|
|VNG0023H||hypothetical protein VNG0023H||30, 254, 290|
|VNG0024H||hypothetical protein VNG0024H||111, 254|
|VNG0057H||hypothetical protein VNG0057H||26, 254|
|VNG0058H||hypothetical protein VNG0058H||254, 270|
|VNG0065G||gmd||GDP-D-mannose dehydratase||164, 254, 280|
|VNG0068H||hypothetical protein VNG0068H||254, 267|
|VNG0073C||hypothetical protein VNG0073C||97, 254|
|VNG0076H||hypothetical protein VNG0076H||28, 254|
|VNG0080H||hypothetical protein VNG0080H||143, 254|
|VNG0085G||moaA||hypothetical protein VNG0085G||254, 267|
|VNG0086Gm||moeA2||putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein||254, 264|
|VNG0091C||hypothetical protein VNG0091C||254|
|VNG0108G||rmeR||RmeR||116, 247, 254|
|VNG0113H||hypothetical protein VNG0113H||111, 254|
|VNG0123G||trp1||ABC transport protein||254, 270|
|VNG0124C||hypothetical protein VNG0124C||254, 270|
|VNG0139H||hypothetical protein VNG0139H||17, 18, 30, 196|
|VNG0140H||hypothetical protein VNG0140H||18, 26, 30, 239|
|VNG0142C||hypothetical protein VNG0142C||254, 267|
|VNG0196H||hypothetical protein VNG0196H||30, 267, 281|
|VNG0277G||crtI3||phytoene dehydrogenase||254, 268|
|VNG0297H||hypothetical protein VNG0297H||254, 270|
|VNG0469H||hypothetical protein VNG0469H||30, 91|
|VNG0470G||trp3||daunorubicin resistance ABC transporter ATP-binding protein||30, 91|
|VNG0532H||hypothetical protein VNG0532H||30, 70, 108|
|VNG0811H||hypothetical protein VNG0811H||30, 87, 138, 147|
|VNG0926H||hypothetical protein VNG0926H||30, 108|
|VNG1209G||hutG||formiminoglutamate hydrolase||254, 284|
|VNG1270H||hypothetical protein VNG1270H||18, 30, 37, 42|
|VNG1271H||hypothetical protein VNG1271H||18, 30, 37|
|VNG1646G||trpG1||anthranilate synthase subunit beta||30, 48, 64, 87|
|VNG1648G||trpF||hypothetical protein VNG1648G||4, 5, 28, 30, 48, 64, 87|
|VNG1649G||trpD||anthranilate phosphoribosyltransferase||28, 30, 48, 64, 87, 92|
|VNG1650H||hypothetical protein VNG1650H||4, 5, 30, 34, 35, 245, 295|
|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|
|VNG1986C||hypothetical protein VNG1986C||17, 26, 30, 31, 108|
|VNG2059H||hypothetical protein VNG2059H||254|
|VNG2097C||hypothetical protein VNG2097C||254|
|VNG6191H||hypothetical protein VNG6191H||17, 30, 34, 38, 41, 44, 80, 91|
|VNG6196G||phoT2||sodium-dependent phosphate transporter||30, 36, 41, 80, 87, 89|
|VNG6258C||hypothetical protein VNG6258C||18, 30, 108|
|VNG6292C||hypothetical protein VNG6292C||17, 18, 30, 89|
|VNG6390H||hypothetical protein VNG6390H||4, 26, 30, 34, 35, 245, 295|
|VNG6400H||hypothetical protein VNG6400H||18, 30, 80, 133, 245, 290|
|VNG6427H||hypothetical protein VNG6427H||17, 18, 30, 62, 74, 89, 107|
|VNG6431H||hypothetical protein VNG6431H||17, 26, 30, 38, 178|
|VNG7011||repH||plasmid replication protein RepH||17, 18, 30, 107, 122, 224, 287|
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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