Organism : Halobacterium salinarum NRC-1 | Module List :
VNG6409H

hypothetical protein VNG6409H

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG6409H
(Mouseover regulator name to see its description)

VNG6409H is regulated by 28 influences and regulates 0 modules.
Regulators for VNG6409H (28)
Regulator Module Operator
VNG1237C 203 tf
VNG1510C 203 tf
VNG2112C 203 tf
VNG6143H 203 tf
VNG1179C 85 tf
VNG1548C 85 tf
VNG1617H
VNG0389C
85 combiner
VNG2112C 85 tf
VNG5163G 85 tf
VNG6143H 85 tf
KO_1_VNG_VNG0716G 153 ef
VNG5068G
VNG0147C
153 combiner
VNG6143H 153 tf
VNG2112C 158 tf
VNG5163G 158 tf
VNG6287H 158 tf
VNG6438G 158 tf
VNG0147C
VNG6288C
160 combiner
VNG1510C
VNG6288C
160 combiner
VNG1548C 160 tf
VNG6143H 160 tf
VNG0869G 152 tf
VNG2112C 152 tf
VNG6438G 152 tf
VNG1548C 198 tf
VNG6143H 198 tf
VNG6387H 198 tf
VNG6438G 198 tf

Warning: VNG6409H Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 14 motifs predicted.

Motif Table (14)
Motif Id e-value Consensus Motif Logo
1145 1.70e+01 taat..acAAa.gtatgcgtagt.
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1146 8.80e+01 AtCgtcaGTaaTg
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1269 2.50e+02 AagaCGTt.aAcGCcgcccTa
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1270 9.10e+02 GtGACGATGaC
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1271 2.90e+02 GaATtCAtg.tAtCG.CA
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1272 1.30e+02 tcGca.g.gaat.Actacgca
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1279 7.30e+00 GTcGtAcaaCaact.aTca.t
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1280 3.10e+03 CGAgaAaC
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1281 5.00e+01 CgtCGaCg.t.tccaCatcaA
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1282 5.10e+02 cgtCtaCGAa
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1349 5.80e+02 AtaTAt.gt.GAAA
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1350 1.80e+03 AATaCGcAaTTCGA
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1355 1.70e+01 acgcTG.tct.tcttgc.Aacaa
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1356 1.10e+03 actgT.GgTtctg
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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 VNG6409H

Warning: No Functional annotations were found!

Module neighborhood information for VNG6409H

VNG6409H has total of 41 gene neighbors in modules 85, 152, 153, 158, 160, 198, 203
Gene neighbors (41)
Gene Common Name Description Module membership
VNG0187H hypothetical protein VNG0187H 160
VNG0189C hypothetical protein VNG0189C 54, 203
VNG0306C hypothetical protein VNG0306C 158, 267
VNG0318G dpg dolichol-P-glucose synthetase 118, 160, 232, 243
VNG0664G birL biotin acetyl-CoA carboxylase ligase 160
VNG0725H hypothetical protein VNG0725H 160
VNG0851C hypothetical protein VNG0851C 160, 284
VNG0988H hypothetical protein VNG0988H 42, 68, 107, 203, 207, 210
VNG1287C hypothetical protein VNG1287C 131, 160
VNG1589C hypothetical protein VNG1589C 4, 5, 8, 28, 69, 85, 204
VNG1984G rnhB ribonuclease HII 160
VNG1992G pgi peroxidase / catalase 198
VNG2032Gm FAD1 enoyl-CoA hydratase 85
VNG2177H hypothetical protein VNG2177H 153
VNG2298H hypothetical protein VNG2298H 42, 68, 152
VNG2299H hypothetical protein VNG2299H 152
VNG2301G txrB3 thioredoxin reductase 152
VNG2512G epf1 mRNA 3'-end processing factor-like protein 158
VNG2562H hypothetical protein VNG2562H 152
VNG2637H hypothetical protein VNG2637H 158
VNG5120H None 18, 37, 198
VNG6005H hypothetical protein VNG6005H 37, 198
VNG6165H hypothetical protein VNG6165H 85
VNG6170H hypothetical protein VNG6170H 4, 5, 15, 26, 28, 31, 36, 53, 60, 63, 69, 72, 85, 122
VNG6171H hypothetical protein VNG6171H 85
VNG6173C hypothetical protein VNG6173C 85
VNG6211G bdb L-2,4-diaminobutyrate decarboxylase 54, 112, 152
VNG6212G iucA iron transport protein A 112, 152
VNG6290H hypothetical protein VNG6290H 158
VNG6343H hypothetical protein VNG6343H 47, 69, 85
VNG6348H hypothetical protein VNG6348H 85, 86, 106, 160, 209
VNG6362G polB2 DNA polymerase B2 203
VNG6384H hypothetical protein VNG6384H 20, 131, 160, 232
VNG6409H hypothetical protein VNG6409H 85, 152, 153, 158, 160, 198, 203
VNG6412H hypothetical protein VNG6412H 103, 198, 203
VNG6413H hypothetical protein VNG6413H 103, 203
VNG7043 hypothetical protein VNG7043 153, 207
VNG7044 hypothetical protein VNG7044 47, 153, 207
VNG7097 hypothetical protein VNG7097 56, 160
VNG7116 hypothetical protein VNG7116 158
VNG7118 hypothetical protein VNG7118 153
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 VNG6409H
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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