Organism : Halobacterium salinarum NRC-1 | Module List :
VNG2011G thiL

hypothetical protein VNG2011G

CircVis
Functional Annotations (6)
Function System
Thiamine monophosphate kinase cog/ cog
thiamine-phosphate kinase activity go/ molecular_function
thiamine biosynthetic process go/ biological_process
Thiamine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
thiL tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG2011G
(Mouseover regulator name to see its description)

VNG2011G is regulated by 16 influences and regulates 0 modules.
Regulators for VNG2011G thiL (16)
Regulator Module Operator
VNG1377G 88 tf
VNG1616C 88 tf
VNG1843C 88 tf
VNG1899G
VNG0258H
88 combiner
VNG1899G
VNG1029C
88 combiner
VNG6351G
VNG2614H
88 combiner
VNG1616C 206 tf
VNG2614H
VNG6387H
206 combiner
VNG1548C 179 tf
VNG1616C 179 tf
VNG1786H 179 tf
VNG1843C 179 tf
VNG2277H 179 tf
VNG2614H
VNG6387H
179 combiner
VNG5068G
VNG1886C
179 combiner
VNG6351G
VNG2614H
179 combiner

Warning: VNG2011G Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 6 motifs predicted.

Motif Table (6)
Motif Id e-value Consensus Motif Logo
1151 2.00e-06 cg.CG.cCgCG...tcGaCg.cGa
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1152 2.00e+04 CGgCGCggcCGgCga
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1317 6.40e-03 AC.ttaa.cA..AgaGatTtT
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1318 6.30e+02 attgaAAtGaAgcgGcGAagA
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1361 1.00e+04 CAcACCagCGA
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1362 1.30e+04 A.CtCaTCGtt
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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 VNG2011G

VNG2011G is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Thiamine monophosphate kinase cog/ cog
thiamine-phosphate kinase activity go/ molecular_function
thiamine biosynthetic process go/ biological_process
Thiamine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
thiL tigr/ tigrfam
Module neighborhood information for VNG2011G

VNG2011G has total of 34 gene neighbors in modules 88, 179, 206
Gene neighbors (34)
Gene Common Name Description Module membership
VNG0598C hypothetical protein VNG0598C 88, 206
VNG0600C hypothetical protein VNG0600C 88, 282
VNG0857Cm RNA methylase 44, 88
VNG1069C hypothetical protein VNG1069C 190, 206, 299
VNG1101C hypothetical protein VNG1101C 129, 173, 206
VNG1112H hypothetical protein VNG1112H 173, 179, 280
VNG1117C hypothetical protein VNG1117C 88
VNG1163G hemK hypothetical protein VNG1163G 88, 154
VNG1164C hypothetical protein VNG1164C 88, 154
VNG1204G gdhA2 hypothetical protein VNG1204G 88, 154, 179
VNG1205C N-ethylammeline chlorohydrolase 179, 285
VNG1319H hypothetical protein VNG1319H 88
VNG1811G eye succinoglycan biosynthesis 42, 68, 179, 286
VNG1814G carB carbamoyl phosphate synthase large subunit 179
VNG1948H hypothetical protein VNG1948H 88
VNG2011G thiL hypothetical protein VNG2011G 88, 179, 206
VNG2049C hypothetical protein VNG2049C 88
VNG2128C tRNA-modifying enzyme 145, 206
VNG2210G endA tRNA splicing endonuclease 88
VNG2211H hypothetical protein VNG2211H 88
VNG2213G brr2 pre-mRNA splicing helicase 88
VNG2269G tatC1 protein export 88
VNG2331G uroM S-adenosyl-L-methionine:uroporphyrinogen III methyltransferase 88, 296
VNG2332G hemD uroporphyrinogen-III synthase 88, 296
VNG2515H hypothetical protein VNG2515H 88, 287, 296
VNG2516C hypothetical protein VNG2516C 88, 129, 173, 206, 287
VNG2536C hypothetical protein VNG2536C 88, 101
VNG2570G dcd deoxyuridine 5'-triphosphate nucleotidohydrolase 129, 179
VNG2586C F420-0--gamma-glutamyl ligase 53, 206
VNG2669G cyo cytochrome oxidase subunit I-like protein 44, 179
VNG6269C hypothetical protein VNG6269C 179
VNG6302C hypothetical protein VNG6302C 83, 206
VNG7033 hypothetical protein VNG7033 97, 179
VNG7034 hypothetical protein VNG7034 97, 179
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 VNG2011G
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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