Organism : Halobacterium salinarum NRC-1 | Module List :
VNG0318G dpg

dolichol-P-glucose synthetase

CircVis
Functional Annotations (2)
Function System
Predicted integral membrane protein cog/ cog
TIGR00374 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG0318G
(Mouseover regulator name to see its description)

VNG0318G is regulated by 19 influences and regulates 0 modules.
Regulators for VNG0318G dpg (19)
Regulator Module Operator
VNG0147C
VNG6288C
232 combiner
VNG1510C 232 tf
VNG1510C
VNG6288C
232 combiner
VNG1548C 232 tf
VNG1786H 232 tf
VNG5176C
VNG6288C
232 combiner
VNG6389G 232 tf
VNG0147C
VNG6288C
160 combiner
VNG1510C
VNG6288C
160 combiner
VNG1548C 160 tf
VNG6143H 160 tf
VNG0462C 118 tf
VNG1886C 118 tf
VNG0147C
VNG6288C
243 combiner
VNG1510C
VNG6288C
243 combiner
VNG1548C 243 tf
VNG5142G 243 tf
VNG5176C
VNG6288C
243 combiner
VNG6389G 243 tf

Warning: VNG0318G Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 8 motifs predicted.

Motif Table (8)
Motif Id e-value Consensus Motif Logo
1209 2.40e-01 CGAcctCGgcG
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1210 2.20e+04 t.aC.gTgagctAgCC.aca
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1281 5.00e+01 CgtCGaCg.t.tccaCatcaA
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1282 5.10e+02 cgtCtaCGAa
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1401 1.60e+03 tcCatccactAaCAa
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1402 8.00e+03 ATTTGTA
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1421 4.20e+00 TggATAaAgAA
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1422 2.90e+03 cTcg.taaCaGtaacT.ctA
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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 VNG0318G

VNG0318G is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted integral membrane protein cog/ cog
TIGR00374 tigr/ tigrfam
Module neighborhood information for VNG0318G

VNG0318G has total of 58 gene neighbors in modules 118, 160, 232, 243
Gene neighbors (58)
Gene Common Name Description Module membership
VNG0025H hypothetical protein VNG0025H 118, 267
VNG0027H hypothetical protein VNG0027H 26, 31, 72, 232, 243
VNG0117H hypothetical protein VNG0117H 72, 207, 209, 243, 298
VNG0170Cm polyketide biosynthesis dithiol-disulfide isomerase 118
VNG0187H hypothetical protein VNG0187H 160
VNG0205H hypothetical protein VNG0205H 118, 267
VNG0268C hypothetical protein VNG0268C 118
VNG0284C hypothetical protein VNG0284C 118, 151
VNG0300C hypothetical protein VNG0300C 118, 126
VNG0305G trpC hypothetical protein VNG0305G 118
VNG0307G trpB tryptophan synthase subunit beta 118, 249
VNG0308Gm trpA tryptophan synthase subunit alpha 118, 249
VNG0314G aroD 3-dehydroquinate dehydratase 118, 151
VNG0318G dpg dolichol-P-glucose synthetase 118, 160, 232, 243
VNG0346H hypothetical protein VNG0346H 118, 269
VNG0364G yusZ3 oxidoreductase 118, 233
VNG0367H hypothetical protein VNG0367H 118, 269
VNG0378C hypothetical protein VNG0378C 118, 282
VNG0396C hypothetical protein VNG0396C 26, 57, 243
VNG0502G aspB1 aspartate aminotransferase 118
VNG0612H hypothetical protein VNG0612H 26, 243
VNG0664G birL biotin acetyl-CoA carboxylase ligase 160
VNG0725H hypothetical protein VNG0725H 160
VNG0763G ybjG membrane protein 57, 243
VNG0777G taqD glycerol-3-phosphate cytidyltransferase 118
VNG0799C hypothetical protein VNG0799C 118, 151
VNG0818C hypothetical protein VNG0818C 86, 106, 243, 298
VNG0851C hypothetical protein VNG0851C 160, 284
VNG0908G putP hypothetical protein VNG0908G 118, 162, 246
VNG0914H hypothetical protein VNG0914H 118
VNG1000H hypothetical protein VNG1000H 20, 26, 31, 232
VNG1287C hypothetical protein VNG1287C 131, 160
VNG1341G fabG 3-oxoacyl- 118, 214
VNG1382H hypothetical protein VNG1382H 118, 274
VNG1429C 2-phospho-L-lactate transferase 31, 232, 243
VNG1681C hypothetical protein VNG1681C 20, 26, 28, 31, 147, 232
VNG1785G panF hypothetical protein VNG1785G 57, 86, 232, 243, 298
VNG1869C hypothetical protein VNG1869C 118, 155, 157
VNG1896C hypothetical protein VNG1896C 118
VNG1957G tgtA2 archaeosine tRNA-ribosyltransferase 118, 129, 130, 132
VNG1974H hypothetical protein VNG1974H 118, 286
VNG1984G rnhB ribonuclease HII 160
VNG1989H hypothetical protein VNG1989H 118
VNG2002H hypothetical protein VNG2002H 26, 232
VNG2003G truA tRNA pseudouridine synthase A 118, 280
VNG2156C hypothetical protein VNG2156C 57, 106, 209, 243, 298
VNG6052H hypothetical protein VNG6052H 118
VNG6143H hypothetical protein VNG6143H 5, 26, 31, 72, 86, 106, 204, 232, 243, 295, 298
VNG6145H hypothetical protein VNG6145H 31, 72, 86, 106, 232, 298
VNG6189H hypothetical protein VNG6189H 118, 286
VNG6339H hypothetical protein VNG6339H 26, 31, 69, 86, 106, 204, 232
VNG6348H hypothetical protein VNG6348H 85, 86, 106, 160, 209
VNG6384H hypothetical protein VNG6384H 20, 131, 160, 232
VNG6409H hypothetical protein VNG6409H 85, 152, 153, 158, 160, 198, 203
VNG6432H hypothetical protein VNG6432H 17, 26, 31, 38, 106, 243
VNG6439H hypothetical protein VNG6439H 26, 31, 243
VNG7056 hypothetical protein VNG7056 86, 105, 106, 186, 209, 232, 238, 243, 257, 298
VNG7097 hypothetical protein VNG7097 56, 160
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 VNG0318G
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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