Organism : Halobacterium salinarum NRC-1 | Module List :
Regulation information for VNG0943C(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|
Module neighborhood information for VNG0943C
|Gene||Common Name||Description||Module membership|
|VNG0019H||hypothetical protein VNG0019H||284|
|VNG0049H||hypothetical protein VNG0049H||192, 253|
|VNG0089G||pimT1||L-isoaspartyl protein carboxyl methyltransferase||253|
|VNG0156C||hypothetical protein VNG0156C||253|
|VNG0179C||hypothetical protein VNG0179C||192, 284|
|VNG0274C||hypothetical protein VNG0274C||253|
|VNG0327G||gadD||L-tyrosine decarboxylase||253, 270|
|VNG0374G||nusG||transcription antitermination protein NusG||253|
|VNG0481G||mcmA1||methylmalonyl-CoA mutase subunit alpha||253|
|VNG0483C||hypothetical protein VNG0483C||252, 284|
|VNG0546C||hypothetical protein VNG0546C||253|
|VNG0590H||hypothetical protein VNG0590H||116, 284|
|VNG0660H||hypothetical protein VNG0660H||253|
|VNG0667G||trp4||ABC transporter ATP-binding protein||253|
|VNG0677H||hypothetical protein VNG0677H||284|
|VNG0717H||hypothetical protein VNG0717H||284|
|VNG0719G||araL||L-arabinose operon protein||264, 284|
|VNG0729H||hypothetical protein VNG0729H||192, 284|
|VNG0738H||hypothetical protein VNG0738H||190, 284|
|VNG0750C||hypothetical protein VNG0750C||77, 284|
|VNG0762H||hypothetical protein VNG0762H||284|
|VNG0764C||hypothetical protein VNG0764C||262, 284|
|VNG0769H||hypothetical protein VNG0769H||253|
|VNG0778C||hypothetical protein VNG0778C||192, 284|
|VNG0800H||hypothetical protein VNG0800H||258, 284|
|VNG0851C||hypothetical protein VNG0851C||160, 284|
|VNG0860G||rpoL||DNA-directed RNA polymerase subunit L||253|
|VNG0865C||hypothetical protein VNG0865C||253, 296|
|VNG0874G||traB||hypothetical protein VNG0874G||149, 284|
|VNG0915G||hakA||atrazine chlorohydrolase||269, 284|
|VNG0943C||hypothetical protein VNG0943C||253, 284|
|VNG1007H||hypothetical protein VNG1007H||35, 284|
|VNG1042H||hypothetical protein VNG1042H||116, 284|
|VNG1083G||menF||isochorismate synthase||273, 284|
|VNG1110C||hypothetical protein VNG1110C||253|
|VNG1119H||hypothetical protein VNG1119H||259, 284|
|VNG1174G||nop56/58||nucleolar protein-like protein||57, 284|
|VNG1181G||flaA1b||flagellin A1||258, 284|
|VNG1208G||hutU||urocanate hydratase||220, 284|
|VNG1209G||hutG||formiminoglutamate hydrolase||254, 284|
|VNG1212Gm||hutH||histidine ammonia-lyase||252, 284|
|VNG1262G||eif2b||translation initiation factor IF-2 subunit beta||253|
|VNG1301G||cysK||hypothetical protein VNG1301G||270, 284|
|VNG1486H||hypothetical protein VNG1486H||253|
|VNG1487H||hypothetical protein VNG1487H||253|
|VNG1500H||hypothetical protein VNG1500H||284|
|VNG1591H||hypothetical protein VNG1591H||253|
|VNG1766C||hypothetical protein VNG1766C||253|
|VNG1782C||hypothetical protein VNG1782C||253|
|VNG2045G||gcp||O-sialoglycoprotein endopeptidase/protein kinase||253|
|VNG2047G||rps27ae||30S ribosomal protein S27ae||253|
|VNG2397G||cysA||hypothetical protein VNG2397G||253|
|VNG2577C||hypothetical protein VNG2577C||253|
|VNG5050H||predicted transcriptional regulator; PFAM03551:PadR/MarR family of transcriptional repressors; COG1695:predicted transcriptional regulators (PET=28)||253|
|VNG7069||hypothetical protein VNG7069||253|
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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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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- 5. Module(s) that source gene and target genes belong to
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