Organism : Halobacterium salinarum NRC-1 | Module List :
VNG0064G graD3

glucose-1-phosphate thymidylyltransferase

CircVis
Functional Annotations (6)
Function System
dTDP-glucose pyrophosphorylase cog/ cog
glucose-1-phosphate thymidylyltransferase activity go/ molecular_function
biosynthetic process go/ biological_process
Streptomycin biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG0064G
(Mouseover regulator name to see its description)

VNG0064G is regulated by 17 influences and regulates 0 modules.
Regulators for VNG0064G graD3 (17)
Regulator Module Operator
VNG1617H 293 tf
VNG2112C 293 tf
VNG6143H 293 tf
VNG0247C 280 tf
VNG1510C 280 tf
VNG1548C 280 tf
VNG2579G 280 tf
VNG5068G
VNG1886C
280 combiner
VNG1510C 74 tf
VNG1786H 74 tf
VNG2112C 74 tf
VNG6143H 74 tf
VNG6438G 74 tf
VNG1237C 164 tf
VNG1383G 164 tf
VNG2579G
VNG0389C
164 combiner
VNG6143H 164 tf

Warning: VNG0064G 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
1123 8.80e+00 aCaatAttCa..Ca.At.aca
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1124 2.10e+03 gAagCagTagt
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1289 4.40e-02 CgtGgcgGTTCtta.cAACGcGAA
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1290 5.20e+01 TAATGGGCCTGGATGCAGTCACTA
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1489 1.40e+01 CcgGTTC.cg.tGgT
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1490 3.40e+01 TAATGGGCCTGGATGCAGTCACTA
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1509 3.90e+02 AAA.CAgTt
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1510 1.20e+03 TTACAcAA
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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 VNG0064G

VNG0064G is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
dTDP-glucose pyrophosphorylase cog/ cog
glucose-1-phosphate thymidylyltransferase activity go/ molecular_function
biosynthetic process go/ biological_process
Streptomycin biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Module neighborhood information for VNG0064G

VNG0064G has total of 16 gene neighbors in modules 74, 164, 280, 293
Gene neighbors (16)
Gene Common Name Description Module membership
VNG0062G lpb LPS biosynthesis protein 106, 164
VNG0063G galE2 UDP-glucose 4-epimerase 164, 280, 282
VNG0064G graD3 glucose-1-phosphate thymidylyltransferase 74, 164, 280, 293
VNG0065G gmd GDP-D-mannose dehydratase 164, 254, 280
VNG0731H hypothetical protein VNG0731H 43, 53, 164
VNG0985H hypothetical protein VNG0985H 4, 5, 164
VNG1112H hypothetical protein VNG1112H 173, 179, 280
VNG1548C hypothetical protein VNG1548C 28, 293
VNG1733G htr17 Htr17 64, 74
VNG1734H hypothetical protein VNG1734H 64, 74
VNG1954H hypothetical protein VNG1954H 74
VNG2003G truA tRNA pseudouridine synthase A 118, 280
VNG2257G nce Na+/Ca2+-exchanging protein 293
VNG6176G kdpA potassium-transporting ATPase subunit A 5, 15, 18, 21, 26, 28, 31, 47, 51, 53, 62, 63, 69, 70, 72, 74, 177, 279
VNG6178G kdpC potassium-transporting ATPase C chain 5, 15, 18, 26, 28, 31, 47, 51, 53, 62, 63, 69, 70, 72, 74, 177, 279
VNG6427H hypothetical protein VNG6427H 17, 18, 30, 62, 74, 89, 107
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 VNG0064G
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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