Organism : Halobacterium salinarum NRC-1 | Module List :
Regulation information for VNG6431H
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
VNG1215G VNG6143H |
178 | combiner |
VNG1786H | 178 | tf |
VNG6389G | 178 | tf |
VNG6438G | 178 | tf |
VNG0462C | 38 | tf |
VNG0869G | 38 | tf |
VNG1886C | 38 | tf |
VNG2112C | 38 | tf |
VNG5163G | 38 | tf |
VNG6143H | 38 | tf |
VNG1510C | 26 | tf |
VNG1548C | 26 | tf |
VNG6389G | 26 | tf |
VNG1510C VNG6288C |
17 | combiner |
VNG1786H | 17 | tf |
VNG2112C | 17 | tf |
VNG6143H | 17 | tf |
VNG6389G | 17 | tf |
VNG6438G | 17 | tf |
VNG6438G VNG6288C |
17 | combiner |
VNG1179C | 30 | tf |
VNG1237C | 30 | tf |
VNG1786H | 30 | tf |
VNG2112C | 30 | tf |
VNG6143H | 30 | tf |
VNG6438G | 30 | tf |
Motif information (de novo identified motifs for modules)
There are 10 motifs predicted.
Motif Id | e-value | Consensus | Motif Logo |
---|---|---|---|
1013 | 1.70e-04 | gtt.T.gcTagc.c.gtcTagTTa | |
1014 | 8.40e-02 | a.cGTcttcaTaatGataAca | |
1029 | 2.30e-02 | gtTtcAgcaccGgcTctGaATagA | |
1030 | 6.00e-03 | atACtcttACaaagATAAAgaaGg | |
1037 | 1.10e-03 | aAaagaAAT.tTCTctTCAcgaat | |
1038 | 1.90e-03 | taCgagacaa.gccgacatt.act | |
1053 | 1.00e-06 | TcaccaA..TaAagacGgatGa | |
1054 | 1.20e-01 | cTCTgAAtgAagAcA | |
1315 | 7.10e-02 | gaatACag.Ta.C.a.AtA..ta | |
1316 | 5.80e+02 | CcAaTtacCGaTccAG.CA |
Module neighborhood information for VNG6431H
Gene | Common Name | Description | Module membership |
---|---|---|---|
VNG0020H | hypothetical protein VNG0020H | 30, 108, 247 | |
VNG0022H | hypothetical protein VNG0022H | 30, 254 | |
VNG0023H | hypothetical protein VNG0023H | 30, 254, 290 | |
VNG0027H | hypothetical protein VNG0027H | 26, 31, 72, 232, 243 | |
VNG0057H | hypothetical protein VNG0057H | 26, 254 | |
VNG0139H | hypothetical protein VNG0139H | 17, 18, 30, 196 | |
VNG0140H | hypothetical protein VNG0140H | 18, 26, 30, 239 | |
VNG0196H | hypothetical protein VNG0196H | 30, 267, 281 | |
VNG0396C | hypothetical protein VNG0396C | 26, 57, 243 | |
VNG0469H | hypothetical protein VNG0469H | 30, 91 | |
VNG0470G | trp3 | daunorubicin resistance ABC transporter ATP-binding protein | 30, 91 |
VNG0532H | hypothetical protein VNG0532H | 30, 70, 108 | |
VNG0573C | hypothetical protein VNG0573C | 4, 5, 26, 28 | |
VNG0612H | hypothetical protein VNG0612H | 26, 243 | |
VNG0811H | hypothetical protein VNG0811H | 30, 87, 138, 147 | |
VNG0883H | hypothetical protein VNG0883H | 5, 26 | |
VNG0926H | hypothetical protein VNG0926H | 30, 108 | |
VNG1000H | hypothetical protein VNG1000H | 20, 26, 31, 232 | |
VNG1064H | hypothetical protein VNG1064H | 17, 37, 96, 108 | |
VNG1156G | hsp3 | Hsp3 | 178, 282 |
VNG1270H | hypothetical protein VNG1270H | 18, 30, 37, 42 | |
VNG1271H | hypothetical protein VNG1271H | 18, 30, 37 | |
VNG1455H | hypothetical protein VNG1455H | 26, 31, 57, 86 | |
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 | |
VNG1681C | hypothetical protein VNG1681C | 20, 26, 28, 31, 147, 232 | |
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 | |
VNG1963H | hypothetical protein VNG1963H | 38 | |
VNG1976H | hypothetical protein VNG1976H | 26, 31, 60 | |
VNG1986C | hypothetical protein VNG1986C | 17, 26, 30, 31, 108 | |
VNG2002H | hypothetical protein VNG2002H | 26, 232 | |
VNG2024H | hypothetical protein VNG2024H | 38 | |
VNG2100G | iluA | threonine dehydratase | 5, 20, 26, 28 |
VNG2174H | hypothetical protein VNG2174H | 34, 38, 297 | |
VNG2316C | hypothetical protein VNG2316C | 48, 178 | |
VNG2317G | cbiO1 | cobalt transport ATP-binding protein | 38, 48, 178 |
VNG2414H | hypothetical protein VNG2414H | 18, 38, 64 | |
VNG2444C | hypothetical protein VNG2444C | 17, 28, 31, 38, 173 | |
VNG5150H | None | 38, 42 | |
VNG5168H | None | 38 | |
VNG6143H | hypothetical protein VNG6143H | 5, 26, 31, 72, 86, 106, 204, 232, 243, 295, 298 | |
VNG6150G | orc1 | orc / cell division control protein 6 | 4, 13, 38, 142, 189 |
VNG6152H | hypothetical protein VNG6152H | 4, 13, 15, 26, 31, 37, 142, 189, 272, 281, 297 | |
VNG6160H | hypothetical protein VNG6160H | 38 | |
VNG6168H | hypothetical protein VNG6168H | 38, 42 | |
VNG6170H | hypothetical protein VNG6170H | 4, 5, 15, 26, 28, 31, 36, 53, 60, 63, 69, 72, 85, 122 | |
VNG6176G | kdpA | potassium-transporting ATPase subunit A | 5, 15, 18, 21, 26, 28, 31, 47, 51, 53, 62, 63, 69, 70, 72, 74, 177, 279 |
VNG6178G | kdpC | potassium-transporting ATPase C chain | 5, 15, 18, 26, 28, 31, 47, 51, 53, 62, 63, 69, 70, 72, 74, 177, 279 |
VNG6191H | hypothetical protein VNG6191H | 17, 30, 34, 38, 41, 44, 80, 91 | |
VNG6193H | hypothetical protein VNG6193H | 17, 32, 34, 38, 41, 42, 44, 80 | |
VNG6196G | phoT2 | sodium-dependent phosphate transporter | 30, 36, 41, 80, 87, 89 |
VNG6197H | hypothetical protein VNG6197H | 38, 108 | |
VNG6229G | gvpL2 | GvpL protein, cluster B | 38, 141, 188 |
VNG6244G | gvpN2 | GvpN protein, cluster B | 5, 26, 53, 185 |
VNG6258C | hypothetical protein VNG6258C | 18, 30, 108 | |
VNG6291H | hypothetical protein VNG6291H | 38 | |
VNG6292C | hypothetical protein VNG6292C | 17, 18, 30, 89 | |
VNG6293C | hypothetical protein VNG6293C | 17 | |
VNG6322H | hypothetical protein VNG6322H | 17, 168, 178 | |
VNG6323H | hypothetical protein VNG6323H | 117, 168, 178 | |
VNG6339H | hypothetical protein VNG6339H | 26, 31, 69, 86, 106, 204, 232 | |
VNG6344H | hypothetical protein VNG6344H | 17, 41 | |
VNG6349C | hypothetical protein VNG6349C | 17 | |
VNG6359H | hypothetical protein VNG6359H | 17, 157, 271 | |
VNG6390H | hypothetical protein VNG6390H | 4, 26, 30, 34, 35, 245, 295 | |
VNG6396H | hypothetical protein VNG6396H | 38 | |
VNG6397H | hypothetical protein VNG6397H | 38 | |
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 | |
VNG6432H | hypothetical protein VNG6432H | 17, 26, 31, 38, 106, 243 | |
VNG6439H | hypothetical protein VNG6439H | 26, 31, 243 | |
VNG7011 | repH | plasmid replication protein RepH | 17, 18, 30, 107, 122, 224, 287 |
VNG7109 | hypothetical protein VNG7109 | 4, 18, 38, 91 | |
VNG7110 | hypothetical protein VNG7110 | 18, 38, 91, 147 |
Gene Page Help
Network Tab
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.
Motifs Tab
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.
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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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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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CircVis
Our 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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