Organism : Halobacterium salinarum NRC-1
| Module List :
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Regulation information for VNG0216H
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
VNG0247C | 32 | tf |
VNG1237C | 32 | tf |
VNG6143H | 32 | tf |
VNG1510C | 20 | tf |
VNG1548C | 20 | tf |
VNG2112C | 20 | tf |
VNG6143H | 20 | tf |
VNG0869G | 93 | tf |
VNG6143H | 93 | tf |
VNG6438G | 93 | tf |
VNG6143H | 92 | tf |
VNG1510C | 94 | tf |
VNG1510C VNG6288C |
94 | combiner |
VNG6143H | 94 | tf |
VNG1786H | 103 | tf |
VNG2112C | 103 | tf |
VNG5068G VNG1886C |
103 | combiner |
VNG6143H | 103 | tf |
VNG0247C | 43 | tf |
VNG1179C | 43 | tf |
VNG1237C | 43 | tf |
VNG1510C | 43 | tf |
VNG1548C | 43 | tf |
VNG6143H | 43 | tf |
VNG1510C VNG6288C |
105 | combiner |
VNG6143H | 105 | tf |
VNG0826C VNG1237C |
104 | combiner |
VNG1179C | 104 | tf |
VNG1510C VNG6288C |
104 | combiner |
VNG2112C | 104 | tf |
VNG6143H | 104 | tf |
VNG1237C | 4 | tf |
VNG2112C | 4 | tf |
VNG6143H | 4 | tf |
VNG1237C | 13 | tf |
VNG2112C | 13 | tf |
VNG6143H | 13 | tf |
VNG6287H | 13 | tf |
VNG6438G | 13 | tf |
VNG1179C | 15 | tf |
VNG1237C | 15 | tf |
VNG6143H | 15 | tf |
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Motif information (de novo identified motifs for modules)
There are 24 motifs predicted.
Motif Id | e-value | Consensus | Motif Logo |
---|---|---|---|
987 | 3.00e-03 | aAaAc.Acg.cCtagctaaaatAa |
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988 | 8.90e-01 | GtCTTggGCGAaTaGAAAtCTTCt |
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1005 | 1.20e+01 | CGaccgagagGAacgcgtGGA |
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1006 | 8.20e+00 | GTtTGAgGTGcgtGAcACGATTC |
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1009 | 1.40e-04 | AAATatAAAtaAgat |
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1010 | 2.50e-03 | AaGtctAtTttgAGtgAAtGggA |
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1019 | 5.40e+03 | tTCtGTTC |
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1020 | 2.80e+03 | gCGaCgGcGAG |
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1041 | 9.60e+00 | acTc.tgatTaAcA |
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1042 | 2.00e+01 | AcAcAcacgAgAcTg.gattA |
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1063 | 8.80e-01 | AcgAAtaGCtgtcCg |
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1064 | 1.80e+01 | T.cacaAc.aCgC.caagTcAcaA |
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1159 | 4.90e-01 | TAtgAAg.ATG |
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1160 | 7.80e+00 | gacactgAaAtTaa.cgt.Tt |
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1161 | 1.10e+01 | Cat.ctTctGtttat |
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1162 | 3.80e+00 | TgtaaTTaaC |
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1163 | 1.10e-02 | ttAaTTa.Cg.TGTgAatca |
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1164 | 1.20e-02 | AatAatG.accGagAaaA.ctAa |
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1179 | 8.50e+01 | TGTAatT |
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1180 | 1.50e+02 | aTttggAg.gaaA.a |
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1181 | 4.30e+02 | A.TGaAaTTa |
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1182 | 1.00e+02 | AatAagaaTa |
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1183 | 4.00e-04 | ttTAtgAAGgAt |
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1184 | 1.00e+00 | AAaACAaGAtT |
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Module neighborhood information for VNG0216H
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 | |
VNG0181G | lpl | Lpl | 32, 43 |
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 | |
VNG0429H | hypothetical protein VNG0429H | 43 | |
VNG0573C | hypothetical protein VNG0573C | 4, 5, 26, 28 | |
VNG0730C | hypothetical protein VNG0730C | 43 | |
VNG0731H | hypothetical protein VNG0731H | 43, 53, 164 | |
VNG0825C | hypothetical protein VNG0825C | 4, 5, 32, 43 | |
VNG0985H | hypothetical protein VNG0985H | 4, 5, 164 | |
VNG1000H | hypothetical protein VNG1000H | 20, 26, 31, 232 | |
VNG1066C | hypothetical protein VNG1066C | 13, 96, 102, 108 | |
VNG1365C | hypothetical protein VNG1365C | 103, 104, 214 | |
VNG1370G | btuC | corrinoid ABC transporter permease | 11, 95, 104 |
VNG1371Gm | btuD | corrinoid ABC transporter ATPase | 95, 103, 104, 214 |
VNG1372C | hypothetical protein VNG1372C | 95, 104, 214 | |
VNG1395G | htr9 | Htr9 | 13, 60, 281 |
VNG1453H | hypothetical protein VNG1453H | 4, 28 | |
VNG1520G | mutY | A/G specific adenine glycosylase, repair protein | 4, 5, 53 |
VNG1577C | hypothetical protein VNG1577C | 20, 53, 96, 140, 173 | |
VNG1580H | hypothetical protein VNG1580H | 20, 53, 140, 173, 277 | |
VNG1581C | hypothetical protein VNG1581C | 20, 140, 173 | |
VNG1582G | hisC2 | hypothetical protein VNG1582G | 20, 53, 96, 140, 173 |
VNG1589C | hypothetical protein VNG1589C | 4, 5, 8, 28, 69, 85, 204 | |
VNG1590H | hypothetical protein VNG1590H | 13, 281 | |
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 | |
VNG1682C | ubiA | prenyltransferase | 20 |
VNG1687C | hypothetical protein VNG1687C | 20, 249 | |
VNG1890H | hypothetical protein VNG1890H | 18, 105, 167 | |
VNG1918C | geranylgeranylglyceryl phosphate synthase-like protein | 13, 20, 53, 60 | |
VNG1953C | hypothetical protein VNG1953C | 13, 18, 30, 34, 42, 80, 91, 108, 115, 121 | |
VNG1971G | gpdB | anaerobic glycerol-3-phosphate dehydrogenase subunit B | 20, 44 |
VNG1982C | putative pseudouridylate synthase | 43 | |
VNG2096G | cctB | thermosome subunit beta | 4, 5, 28, 53, 140, 173 |
VNG2100G | iluA | threonine dehydratase | 5, 20, 26, 28 |
VNG2123G | nhaC2 | Na+/H+ antiporter | 94 |
VNG2285C | hypothetical protein VNG2285C | 95, 104 | |
VNG2286G | mamA | methylaspartate mutase subunit S | 94, 95, 104, 105 |
VNG2288G | mamB | methylaspartate mutase | 94, 95, 104 |
VNG2289G | mal | methylaspartate ammonia-lyase | 104 |
VNG2290G | maoC1 | monoamine oxidase regulatory-like | 94, 95, 104 |
VNG2291G | cat | 4-hydroxybutyrate CoA transferase | 92, 94, 95, 104, 105 |
VNG2386C | hypothetical protein VNG2386C | 13, 28 | |
VNG2454C | hypothetical protein VNG2454C | 32 | |
VNG2466C | None | 13, 31, 64, 70, 166 | |
VNG5047H | None | 15, 18, 63 | |
VNG5073H | None | 13 | |
VNG6144G | trsE | transfer complex protein | 4, 5, 42, 68, 295 |
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 | |
VNG6170H | hypothetical protein VNG6170H | 4, 5, 15, 26, 28, 31, 36, 53, 60, 63, 69, 72, 85, 122 | |
VNG6175G | trkA2 | TRK potassium uptake system protein | 5, 15, 62, 69, 72, 177 |
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 |
VNG6177G | kdpB | potassium-transporting ATPase subunit B | 5, 15, 62, 63, 69, 72 |
VNG6178G | kdpC | potassium-transporting ATPase C chain | 5, 15, 18, 26, 28, 31, 47, 51, 53, 62, 63, 69, 70, 72, 74, 177, 279 |
VNG6183C | hypothetical protein VNG6183C | 15, 18, 213 | |
VNG6184G | cat4 | cationic amino acid transporter | 15, 18, 213 |
VNG6185H | hypothetical protein VNG6185H | 15, 18, 213 | |
VNG6186H | hypothetical protein VNG6186H | 15, 18, 213 | |
VNG6193H | hypothetical protein VNG6193H | 17, 32, 34, 38, 41, 42, 44, 80 | |
VNG6230G | gvpK2 | GvpK protein, cluster B | 4, 5, 8, 22, 28, 31, 141, 148, 181, 182, 188, 200 |
VNG6232G | gvpJ2 | GvpJ protein, cluster B | 4, 5, 8, 28, 31, 42, 141, 148, 182, 188 |
VNG6239G | gvpE2 | GvpE protein, cluster B | 4, 5, 8, 28, 141, 148, 182, 188, 200 |
VNG6297C | hypothetical protein VNG6297C | 105, 207 | |
VNG6340H | hypothetical protein VNG6340H | 62, 92, 93, 94, 96, 102, 103, 104 | |
VNG6375H | hypothetical protein VNG6375H | 13, 60, 121, 189 | |
VNG6377H | hypothetical protein VNG6377H | 13, 60, 121, 189 | |
VNG6378H | hypothetical protein VNG6378H | 13, 21, 53, 60, 121, 189, 281 | |
VNG6383G | lctP | L-lactate permease | 8, 13, 14 |
VNG6384H | hypothetical protein VNG6384H | 20, 131, 160, 232 | |
VNG6390H | hypothetical protein VNG6390H | 4, 26, 30, 34, 35, 245, 295 | |
VNG6412H | hypothetical protein VNG6412H | 103, 198, 203 | |
VNG6413H | hypothetical protein VNG6413H | 103, 203 | |
VNG6416H | hypothetical protein VNG6416H | 13, 15, 21, 41, 60, 281 | |
VNG6418H | hypothetical protein VNG6418H | 13, 18, 21, 41, 60, 281 | |
VNG6419H | hypothetical protein VNG6419H | 13, 21, 60, 281 | |
VNG6424H | hypothetical protein VNG6424H | 13, 15, 189 | |
VNG7046 | hypothetical protein VNG7046 | 13, 212, 216 | |
VNG7052 | hypothetical protein VNG7052 | 13 | |
VNG7056 | hypothetical protein VNG7056 | 86, 105, 106, 186, 209, 232, 238, 243, 257, 298 | |
VNG7058 | hypothetical protein VNG7058 | 105 | |
VNG7109 | hypothetical protein VNG7109 | 4, 18, 38, 91 | |
VNG7120 | hypothetical protein VNG7120 | 93 |
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.
Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.
Regulation Tab
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.
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.
Help Tab
This help page. More general help can be accessed by clicking help menu in the main navigation bar.
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;![](/static/images/help_images/circvis-help.png)
- 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)
- 4. Interactions between source and target genes for a particular module
- 5. Module(s) that source gene and target genes belong to
- 6. Visualisation legend
Social Tab
Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.
Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.
In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.