Organism : Halobacterium salinarum NRC-1 | Module List :
VNG6193H
hypothetical protein VNG6193H
Functional Annotations (3)
Function | System |
---|---|
Antitoxin of toxin-antitoxin stability system | cog/ cog |
DNA binding | go/ molecular_function |
regulation of transcription, DNA-dependent | go/ biological_process |
Regulation information for VNG6193H
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
VNG1179C | 41 | tf |
VNG1237C | 41 | tf |
VNG2112C | 41 | tf |
VNG6143H | 41 | tf |
VNG6389G | 41 | tf |
VNG6438G | 41 | tf |
VNG1548C | 44 | tf |
VNG1616C VNG0389C |
44 | combiner |
VNG1886C | 44 | tf |
VNG6143H | 44 | tf |
VNG2112C | 42 | tf |
VNG6143H | 42 | tf |
VNG6389G | 42 | tf |
VNG1510C | 80 | tf |
VNG2112C | 80 | tf |
VNG6389G | 80 | tf |
VNG6438G | 80 | tf |
VNG1510C VNG6288C |
17 | combiner |
VNG1786H | 17 | tf |
VNG2112C | 17 | tf |
VNG6143H | 17 | tf |
VNG6389G | 17 | tf |
VNG6438G | 17 | tf |
VNG6438G VNG6288C |
17 | combiner |
VNG0247C | 32 | tf |
VNG1237C | 32 | tf |
VNG6143H | 32 | tf |
VNG1510C | 34 | tf |
VNG2112C | 34 | tf |
VNG6143H | 34 | tf |
VNG6438G | 34 | tf |
VNG0462C | 38 | tf |
VNG0869G | 38 | tf |
VNG1886C | 38 | tf |
VNG2112C | 38 | tf |
VNG5163G | 38 | tf |
VNG6143H | 38 | tf |
Module | Residual | Genes |
---|---|---|
86 | 0.33 | 23 |
106 | 0.31 | 15 |
134 | 0.24 | 2 |
149 | 0.25 | 2 |
171 | 0.24 | 2 |
186 | 0.39 | 7 |
219 | 0.29 | 3 |
227 | 0.47 | 28 |
290 | 0.20 | 2 |
298 | 0.36 | 28 |
Motif information (de novo identified motifs for modules)
There are 16 motifs predicted.
Motif Id | e-value | Consensus | Motif Logo |
---|---|---|---|
1013 | 1.70e-04 | gtt.T.gcTagc.c.gtcTagTTa | |
1014 | 8.40e-02 | a.cGTcttcaTaatGataAca | |
1041 | 9.60e+00 | acTc.tgatTaAcA | |
1042 | 2.00e+01 | AcAcAcacgAgAcTg.gattA | |
1045 | 0.00e+00 | aaTAGaaAtCTTCtcTTcAcTGt | |
1046 | 0.00e+00 | AagacCaAtctgatgttaATTcaG | |
1053 | 1.00e-06 | TcaccaA..TaAagacGgatGa | |
1054 | 1.20e-01 | cTCTgAAtgAagAcA | |
1059 | 3.50e+01 | AatttcTctTgcGGAagta | |
1060 | 1.20e+04 | CcacGAcgAaCgCC | |
1061 | 3.40e+00 | acgatCttgtcgt.g | |
1062 | 3.80e+04 | ACTGACAGtaTATGT | |
1065 | 3.40e+03 | taagctCca.accCGGcAcat | |
1066 | 8.30e+03 | ccGCgAAcaaC | |
1135 | 1.50e+03 | aA.at..tTctgcGGaaa.t | |
1136 | 1.50e+03 | CgTCggTTcag |
Functional Enrichment for VNG6193H
Function | System |
---|---|
Antitoxin of toxin-antitoxin stability system | cog/ cog |
DNA binding | go/ molecular_function |
regulation of transcription, DNA-dependent | go/ biological_process |
Module neighborhood information for VNG6193H
Gene | Common Name | Description | Module membership |
---|---|---|---|
VNG0030H | hypothetical protein VNG0030H | 32, 233, 239 | |
VNG0031H | hypothetical protein VNG0031H | 32, 233, 239 | |
VNG0032H | hypothetical protein VNG0032H | 32, 233, 239 | |
VNG0055H | hypothetical protein VNG0055H | 37, 41, 183, 185 | |
VNG0139H | hypothetical protein VNG0139H | 17, 18, 30, 196 | |
VNG0148H | hypothetical protein VNG0148H | 41, 80, 171, 189, 196, 219, 224 | |
VNG0181G | lpl | Lpl | 32, 43 |
VNG0204H | hypothetical protein VNG0204H | 41 | |
VNG0213H | hypothetical protein VNG0213H | 34, 35, 295 | |
VNG0215C | hypothetical protein VNG0215C | 32, 92, 93, 94, 103, 104, 105 | |
VNG0216H | hypothetical protein VNG0216H | 4, 13, 15, 20, 32, 43, 92, 93, 94, 103, 104, 105 | |
VNG0217H | hypothetical protein VNG0217H | 13, 15, 20, 32, 43, 53, 92, 93, 94, 103, 105 | |
VNG0316C | hypothetical protein VNG0316C | 42, 68 | |
VNG0430H | hypothetical protein VNG0430H | 42, 68, 151 | |
VNG0462C | hypothetical protein VNG0462C | 42, 57, 68, 151, 162, 246 | |
VNG0626G | maoC2 | molybdenum cofactor biosynthesis protein | 80 |
VNG0761G | dip3 | competence-damage protein CinA-like | 44, 151, 214 |
VNG0819C | hypothetical protein VNG0819C | 42 | |
VNG0825C | hypothetical protein VNG0825C | 4, 5, 32, 43 | |
VNG0836H | hypothetical protein VNG0836H | 42, 68 | |
VNG0854C | hypothetical protein VNG0854C | 44 | |
VNG0857Cm | RNA methylase | 44, 88 | |
VNG0870G | gatC | hypothetical protein VNG0870G | 42, 68 |
VNG0988H | hypothetical protein VNG0988H | 42, 68, 107, 203, 207, 210 | |
VNG1064H | hypothetical protein VNG1064H | 17, 37, 96, 108 | |
VNG1270H | hypothetical protein VNG1270H | 18, 30, 37, 42 | |
VNG1525C | hypothetical protein VNG1525C | 41 | |
VNG1534a | birA | biotin operon repressor and biotin-(acetyl-CoA carboxylase) ligase | 41 |
VNG1650H | hypothetical protein VNG1650H | 4, 5, 30, 34, 35, 245, 295 | |
VNG1732C | hypothetical protein VNG1732C | 80 | |
VNG1779C | hypothetical protein VNG1779C | 44, 131, 230, 234 | |
VNG1784C | DNA primase | 28, 42, 68, 83, 234 | |
VNG1811G | eye | succinoglycan biosynthesis | 42, 68, 179, 286 |
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 | |
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 | |
VNG1967G | glpK | hypothetical protein VNG1967G | 44 |
VNG1969G | gpdA2 | glycerol-3-phosphate dehydrogenase chain A | 44 |
VNG1971G | gpdB | anaerobic glycerol-3-phosphate dehydrogenase subunit B | 20, 44 |
VNG1986C | hypothetical protein VNG1986C | 17, 26, 30, 31, 108 | |
VNG2024H | hypothetical protein VNG2024H | 38 | |
VNG2034H | hypothetical protein VNG2034H | 41 | |
VNG2174H | hypothetical protein VNG2174H | 34, 38, 297 | |
VNG2185H | hypothetical protein VNG2185H | 41 | |
VNG2298H | hypothetical protein VNG2298H | 42, 68, 152 | |
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 | |
VNG2454C | hypothetical protein VNG2454C | 32 | |
VNG2632G | yusZ2 | oxidoreductase | 34, 41, 143 |
VNG2669G | cyo | cytochrome oxidase subunit I-like protein | 44, 179 |
VNG5150H | None | 38, 42 | |
VNG5168H | None | 38 | |
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 | |
VNG6150G | orc1 | orc / cell division control protein 6 | 4, 13, 38, 142, 189 |
VNG6158H | hypothetical protein VNG6158H | 42, 68 | |
VNG6160H | hypothetical protein VNG6160H | 38 | |
VNG6168H | hypothetical protein VNG6168H | 38, 42 | |
VNG6187G | orc3 | orc / cell division control protein 6 | 42, 68 |
VNG6191H | hypothetical protein VNG6191H | 17, 30, 34, 38, 41, 44, 80, 91 | |
VNG6193H | hypothetical protein VNG6193H | 17, 32, 34, 38, 41, 42, 44, 80 | |
VNG6194H | hypothetical protein VNG6194H | 34 | |
VNG6196G | phoT2 | sodium-dependent phosphate transporter | 30, 36, 41, 80, 87, 89 |
VNG6197H | hypothetical protein VNG6197H | 38, 108 | |
VNG6203H | hypothetical protein VNG6203H | 42 | |
VNG6229G | gvpL2 | GvpL protein, cluster B | 38, 141, 188 |
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 |
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 | |
VNG6325H | hypothetical protein VNG6325H | 80 | |
VNG6327H | hypothetical protein VNG6327H | 41 | |
VNG6344H | hypothetical protein VNG6344H | 17, 41 | |
VNG6349C | hypothetical protein VNG6349C | 17 | |
VNG6359H | hypothetical protein VNG6359H | 17, 157, 271 | |
VNG6389G | tfbE | transcription initiation factor IIB | 34 |
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 | |
VNG6401H | hypothetical protein VNG6401H | 80, 133, 237, 248 | |
VNG6402H | hypothetical protein VNG6402H | 80 | |
VNG6416H | hypothetical protein VNG6416H | 13, 15, 21, 41, 60, 281 | |
VNG6418H | hypothetical protein VNG6418H | 13, 18, 21, 41, 60, 281 | |
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 | |
VNG7011 | repH | plasmid replication protein RepH | 17, 18, 30, 107, 122, 224, 287 |
VNG7013 | hypothetical protein VNG7013 | 80 | |
VNG7073 | hypothetical protein VNG7073 | 34, 35, 245, 295 | |
VNG7109 | hypothetical protein VNG7109 | 4, 18, 38, 91 | |
VNG7110 | hypothetical protein VNG7110 | 18, 38, 91, 147 | |
VNG7138 | hypothetical protein VNG7138 | 34, 35, 245, 295 |
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.
Functions Tab
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.
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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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