Organism : Halobacterium salinarum NRC-1 | Module List :
VNG1464G bat

bacterio-opsin activator

CircVis
Functional Annotations (6)
Function System
FOG: PAS/PAC domain cog/ cog
two-component sensor activity go/ molecular_function
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sensory_box tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG1464G
(Mouseover regulator name to see its description)

VNG1464G is regulated by 64 influences and regulates 8 modules.
Regulators for VNG1464G bat (64)
Regulator Module Operator
VNG0651G 11 tf
VNG1123G
VNG6143H
11 combiner
VNG1922G 11 tf
VNG6288C 11 tf
VNG0039H
VNG1405C
9 combiner
VNG0293H 9 tf
VNG0462C
VNG2641H
9 combiner
VNG0651G
VNG2641H
9 combiner
VNG0835G
VNG1123G
9 combiner
VNG1123G
VNG0156C
9 combiner
VNG1123G
VNG1405C
9 combiner
VNG1405C
VNG2641H
9 combiner
VNG1426H
VNG2641H
9 combiner
VNG5182G 9 tf
VNG0039H
VNG1405C
289 combiner
VNG0039H
VNG1548C
289 combiner
VNG0066H
VNG1405C
289 combiner
VNG0293H 289 tf
VNG0651G 289 tf
VNG1123G
VNG0156C
289 combiner
VNG1123G
VNG6143H
289 combiner
VNG1405C 289 tf
VNG1426H 289 tf
VNG0651G 223 tf
VNG1123G
VNG6143H
223 combiner
VNG1405C 223 tf
VNG1786H
VNG2641H
223 combiner
VNG2184G
VNG1123G
223 combiner
VNG0651G 244 tf
VNG1096H 244 tf
VNG1123G
VNG1510C
244 combiner
VNG1123G
VNG1786H
244 combiner
VNG1405C 244 tf
VNG5182G 244 tf
VNG0039H
VNG1786H
208 combiner
VNG0156C 208 tf
VNG1096H 208 tf
VNG1123G
VNG6143H
208 combiner
VNG1405C 208 tf
VNG0651G 273 tf
VNG1096H 273 tf
VNG1123G
VNG1786H
273 combiner
VNG1816G 273 tf
VNG6288C 273 tf
VNG0039H
VNG1786H
125 combiner
VNG0293H 125 tf
VNG0651G 125 tf
VNG1123G
VNG6143H
125 combiner
VNG1405C 125 tf
VNG0039H
VNG1786H
73 combiner
VNG0293H 73 tf
VNG0651G 73 tf
VNG0835G
VNG1123G
73 combiner
VNG1096H 73 tf
VNG1123G
VNG0156C
73 combiner
VNG1786H
VNG2641H
73 combiner
VNG0254G
VNG0156C
84 combiner
VNG0254G
VNG1405C
84 combiner
VNG0835G
VNG0254G
84 combiner
VNG1123G
VNG0156C
84 combiner
VNG1426H
VNG2641H
84 combiner
VNG1786H
VNG2641H
84 combiner
VNG2641H 84 tf
VNG5182G 84 tf
Regulated by VNG1464G (8)
Module Residual Genes
49 0.32 31
71 0.36 23
128 0.39 6
136 0.60 7
170 0.37 6
187 0.40 23
205 0.51 30
240 0.47 6
Motif information (de novo identified motifs for modules)

There are 20 motifs predicted.

Motif Table (20)
Motif Id e-value Consensus Motif Logo
997 2.30e-05 AcCCAAaCtcATgGGGtaT
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998 1.60e+00 AaTCAatTtacTagAaagaCC
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1001 0.00e+00 acAccCAAacacaTgGgGgaTcgG
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1002 5.00e-04 AAAttGATTGcgtcctgtaGtta
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1121 1.40e-05 AaCACCCAAACacATggGGtaT
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1122 1.10e-03 aaa.tGatTgggtgcTataGtTac
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1143 0.00e+00 aaactgatTggGtgcTttaGtTgC
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1144 3.70e+01 AACacCcAAaCAcAT
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1223 0.00e+00 AaCACCcAAActcATggggtAT
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1224 3.90e-03 CaaA.tgATtggggccT.tagtta
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1365 0.00e+00 caAtaccccAttagttTGgGtgt
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1366 7.90e-04 cCCcAAtCAatctgtTa
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1387 0.00e+00 aacAcCCAAaCtcaTaggggat
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1388 3.60e+01 ACcAAaTtGatTgGggGCTGTaGT
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1423 7.00e-06 acacCCAAACtcaTgGGGtaTcgG
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1424 5.30e+00 CAATTtggTAGaAaCtCCcaCATG
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1479 0.00e+00 atcCcCaatgag.ttGggtgtT.t
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1480 5.80e-03 aggCCCcAAtCAATcTggTa
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1507 3.60e+00 C.aa.tgaTTGgGtccTttag.T
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1508 2.00e+03 GGGTGCGCTgTT
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for VNG1464G

VNG1464G is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
FOG: PAS/PAC domain cog/ cog
two-component sensor activity go/ molecular_function
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sensory_box tigr/ tigrfam
Module neighborhood information for VNG1464G

VNG1464G has total of 65 gene neighbors in modules 9, 11, 73, 84, 125, 208, 223, 244, 273, 289
Gene neighbors (65)
Gene Common Name Description Module membership
VNG0104G serA3 SerA3 223, 244
VNG0168H hypothetical protein VNG0168H 244
VNG0174G cat1 cationic amino acid transporter 9, 223, 244
VNG0195H hypothetical protein VNG0195H 84, 289
VNG0226G htrA hypothetical protein VNG0226G 9, 187
VNG0293H hypothetical protein VNG0293H 84
VNG0402H hypothetical protein VNG0402H 73, 84
VNG0651G imd1 inosine-5'-monophosphate dehydrogenase 208
VNG0654C hypothetical protein VNG0654C 9, 11, 73, 84, 125, 208, 223, 244, 273, 289
VNG0656H hypothetical protein VNG0656H 11, 73, 208, 223, 244, 273
VNG0737H hypothetical protein VNG0737H 9, 244, 273
VNG0828H hypothetical protein VNG0828H 9, 11, 73, 84, 125, 208, 223, 240, 244, 273, 289
VNG0829G dmsA dimethylsulfoxide reductase 9, 11, 73, 84, 125, 208, 223, 240, 244, 273, 289
VNG0830G hmoA HmoA 9, 11, 73, 84, 125, 208, 223, 244, 273, 289
VNG0831G moz molybdopterin oxidoreductase 9, 11, 73, 84, 125, 208, 223, 244, 273, 289
VNG0832C hypothetical protein VNG0832C 9, 11, 73, 84, 125, 208, 223, 244, 273, 289
VNG0997G acs2 acetyl-CoA synthetase 9, 73, 84
VNG1039H hypothetical protein VNG1039H 11, 73, 244, 273
VNG1083G menF isochorismate synthase 273, 284
VNG1120H hypothetical protein VNG1120H 9, 187
VNG1121G aspC2 aspartate aminotransferase 73, 125, 223
VNG1168C hypothetical protein VNG1168C 244
VNG1200H hypothetical protein VNG1200H 9, 73, 84, 223, 244
VNG1213C hypothetical protein VNG1213C 84, 283
VNG1264C hypothetical protein VNG1264C 9, 25, 55, 84
VNG1314H hypothetical protein VNG1314H 9, 84
VNG1315H hypothetical protein VNG1315H 84
VNG1370G btuC corrinoid ABC transporter permease 11, 95, 104
VNG1380H hypothetical protein VNG1380H 9, 73, 84, 223
VNG1405C hypothetical protein VNG1405C 11, 73, 151, 257, 273
VNG1458G crtB1 phytoene synthase 9, 11, 73, 84, 125, 208, 223, 244, 273, 289
VNG1459H hypothetical protein VNG1459H 9, 11, 73, 84, 125, 208, 223, 244, 273, 289
VNG1461H hypothetical protein VNG1461H 9, 11, 73, 84, 125, 208, 223, 244, 273, 289
VNG1462G cdc48a cell division cycle protein 9, 11, 73, 84, 125, 208, 223, 244, 273
VNG1463G blp bacterio-opsin linked protein 9, 11, 73, 84, 125, 208, 223, 244, 273, 289
VNG1464G bat bacterio-opsin activator 9, 11, 73, 84, 125, 208, 223, 244, 273, 289
VNG1465G brp bacteriorhodopsin-like protein 9, 11, 73, 84, 125, 208, 223, 244, 273, 289
VNG1467G bop bacterio-opsin 9, 11, 73, 84, 125, 208, 223, 244, 273, 289
VNG1468H hypothetical protein VNG1468H 9, 11, 73, 84, 125, 208, 223, 244, 273, 289
VNG1536C hypothetical protein VNG1536C 84
VNG1544G clc chloride channel 146, 273
VNG1628G aad aryl-alcohol dehydrogenase 11, 208, 244, 273
VNG1630H hypothetical protein VNG1630H 11, 208, 244, 273
VNG1655H hypothetical protein VNG1655H 11
VNG1656H hypothetical protein VNG1656H 11, 208, 273
VNG1657H hypothetical protein VNG1657H 11, 208, 244, 273
VNG1676G gbp2 GTP-binding protein 84
VNG1754G phr1 photolyase/cryptochrome 208, 223, 273
VNG1755G crtI2 phytoene dehydrogenase 11, 208, 223, 273
VNG1806H hypothetical protein VNG1806H 9, 242
VNG1826H hypothetical protein VNG1826H 9, 73
VNG1834G hyrA HyrA 223
VNG1882G nadA quinolinate synthetase 11, 208, 223, 273
VNG1883G nadB L-aspartate oxidase 11, 73, 125, 208, 223, 244, 273
VNG1884G nadC hypothetical protein VNG1884G 11, 73, 125, 208, 223, 244, 273
VNG2008H hypothetical protein VNG2008H 9, 49, 79, 113, 170, 187
VNG2014H hypothetical protein VNG2014H 9, 73, 208, 223
VNG2137G ggt geranylgeranyl-diphosphate geranylgeranyltransferase 11, 208, 244, 273
VNG2199H hypothetical protein VNG2199H 73
VNG2385H hypothetical protein VNG2385H 223
VNG2413H hypothetical protein VNG2413H 9, 84, 113, 242
VNG2535H hypothetical protein VNG2535H 9, 11, 73, 125, 208, 223, 244, 273
VNG5053H None 9
VNG6199G cdc48d cell division cycle protein 98, 125, 240
VNG6223C hypothetical protein VNG6223C 9, 187
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.

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.

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)
  • 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
Comments for VNG1464G
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

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)
  • 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