Organism : Halobacterium salinarum NRC-1 | Module List :
VNG0821C

hypothetical protein VNG0821C

CircVis
Functional Annotations (2)
Function System
metabolic process go/ biological_process
methyltransferase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG0821C
(Mouseover regulator name to see its description)

VNG0821C is regulated by 3 influences and regulates 0 modules.
Regulators for VNG0821C (3)
Regulator Module Operator
VNG0147C
VNG6288C
258 combiner
VNG1816G 258 tf
VNG6143H 258 tf

Warning: VNG0821C Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 2 motifs predicted.

Motif Table (2)
Motif Id e-value Consensus Motif Logo
1449 1.50e+04 t.GtcGcCgcGgTcG
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1450 7.30e+04 TCAcAGATAA
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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 VNG0821C

VNG0821C is enriched for 2 functions in 2 categories.
Enrichment Table (2)
Function System
metabolic process go/ biological_process
methyltransferase activity go/ molecular_function
Module neighborhood information for VNG0821C

VNG0821C has total of 30 gene neighbors in modules 258
Gene neighbors (30)
Gene Common Name Description Module membership
VNG0431G apa diadenosine tetraphosphate pyrophosphohydrolase 258
VNG0543H hypothetical protein VNG0543H 258
VNG0630G ribH 6,7-dimethyl-8-ribityllumazine synthase 258
VNG0689G trp5 ABC transporter ATP-binding protein 258
VNG0716G afsQ2 sensory histidine protein kinase-like protein 258
VNG0724H hypothetical protein VNG0724H 258
VNG0784G pssA CDP-diacylglycerol-serine O-phosphatidyltransferase 258
VNG0800H hypothetical protein VNG0800H 258, 284
VNG0808G gabD succinate-semialdehyde dehydrogenase 258, 285
VNG0821C hypothetical protein VNG0821C 258
VNG0835G idr2 iron-dependent repressor-like protein 258
VNG0847H hypothetical protein VNG0847H 258
VNG1053G gtl glycosyl transferase-like protein 258
VNG1096H hypothetical protein VNG1096H 258
VNG1181G flaA1b flagellin A1 258, 284
VNG1226H hypothetical protein VNG1226H 258
VNG1514H hypothetical protein VNG1514H 258
VNG1529G mmdA methylmalonyl-CoA decarboxylase subunit alpha 258
VNG1613H hypothetical protein VNG1613H 258
VNG1626C hypothetical protein VNG1626C 258
VNG1679H hypothetical protein VNG1679H 258
VNG1684G crtI1 phytoene dehydrogenase 258
VNG1843C hypothetical protein VNG1843C 258
VNG1851G suk sugar kinase 258
VNG1906H fxsA FxsA 258
VNG2035H hypothetical protein VNG2035H 258
VNG2091H hypothetical protein VNG2091H 258
VNG2168C hypothetical protein VNG2168C 258
VNG2447G lta threonine aldolase 258
VNG2638G bchP geranylgeranyl hydrogenase 258
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 VNG0821C
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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