Organism : Halobacterium salinarum NRC-1 | Module List :
VNG0463C

hypothetical protein VNG0463C

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG0463C
(Mouseover regulator name to see its description)

VNG0463C is regulated by 15 influences and regulates 0 modules.
Regulators for VNG0463C (15)
Regulator Module Operator
VNG1237C 162 tf
VNG1510C 162 tf
VNG1786H 162 tf
VNG2112C 162 tf
VNG0869G 249 tf
VNG5163G 249 tf
VNG6438G 249 tf
VNG1179C 246 tf
VNG1786H 246 tf
VNG2112C 246 tf
VNG5163G 246 tf
VNG0247C 14 tf
VNG0869G 14 tf
VNG1179C 14 tf
VNG2112C 14 tf

Warning: VNG0463C 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
1007 4.20e-02 AgTtACatATGGAtggTTAtGAG
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1008 5.00e-02 ACgAgAgCcaGtAtGAgAACAtTA
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1285 1.30e+03 ACcTCGT
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1286 2.40e+03 ACtaC.cCaCtA.AATccaT
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1427 1.00e+03 cGaCgcgCtCG
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1428 7.30e+03 GaACG.TgTTT
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1431 2.40e+02 ATacAGAtAtAAAcTacTTTATaA
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1432 3.30e+03 ATTTGA
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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 VNG0463C

Warning: No Functional annotations were found!

Module neighborhood information for VNG0463C

VNG0463C has total of 27 gene neighbors in modules 14, 162, 246, 249
Gene neighbors (27)
Gene Common Name Description Module membership
VNG0188H hypothetical protein VNG0188H 246, 265
VNG0307G trpB tryptophan synthase subunit beta 118, 249
VNG0308Gm trpA tryptophan synthase subunit alpha 118, 249
VNG0462C hypothetical protein VNG0462C 42, 57, 68, 151, 162, 246
VNG0463C hypothetical protein VNG0463C 14, 162, 246, 249
VNG0465Gm nosF2 copper transport ATP-binding protein 249
VNG0466C hypothetical protein VNG0466C 14, 249
VNG0838G ssrA integrase/recombinase 249
VNG0840H hypothetical protein VNG0840H 166, 246
VNG0907H hypothetical protein VNG0907H 126, 162, 246
VNG0908G putP hypothetical protein VNG0908G 118, 162, 246
VNG0909H hypothetical protein VNG0909H 162, 246
VNG1266G ogg 8-oxoguanine DNA glycosylase 154, 162
VNG1311G alkA 3-methyladenine DNA glycosylase 246, 285
VNG1317H hypothetical protein VNG1317H 130, 246
VNG1503C hypothetical protein VNG1503C 246, 300
VNG1687C hypothetical protein VNG1687C 20, 249
VNG1891H hypothetical protein VNG1891H 14, 42, 68, 135
VNG1893G trp2 ABC transport protein 14, 42
VNG1894C hypothetical protein VNG1894C 14, 42
VNG2080C hypothetical protein VNG2080C 116, 162
VNG6135C hypothetical protein VNG6135C 162
VNG6262G zurM ABC transporter permease 6, 76, 163, 174, 205, 226, 249
VNG6264G zurA ABC transporter ATP-binding protein 6, 76, 163, 205, 226, 249
VNG6265G ycdH adhesion protein 6, 76, 163, 174, 205, 226, 249
VNG6381H hypothetical protein VNG6381H 14
VNG6383G lctP L-lactate permease 8, 13, 14
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 VNG0463C
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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