Organism : Halobacterium salinarum NRC-1 | Module List :
VNG1377G asnC

transcription regulator

CircVis
Functional Annotations (5)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG1377G
(Mouseover regulator name to see its description)

VNG1377G is regulated by 8 influences and regulates 11 modules.
Regulators for VNG1377G asnC (8)
Regulator Module Operator
VNG0458G
VNG0293H
296 combiner
VNG1843C 296 tf
VNG1899G
VNG0734G
296 combiner
VNG1899G
VNG2641H
296 combiner
VNG0254G 255 tf
VNG0751C 255 tf
VNG2441G
VNG0751C
255 combiner
VNG5028G
VNG0751C
255 combiner

Warning: VNG1377G Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
1443 6.20e+01 ACaCCGacgaC
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1444 5.90e+03 GcTTTtaCG.G
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1513 2.10e+01 GCACcGTCtaC
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1514 2.30e+02 ttcGaCgaCgaGcAggacg
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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 VNG1377G

VNG1377G is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for VNG1377G

VNG1377G has total of 39 gene neighbors in modules 255, 296
Gene neighbors (39)
Gene Common Name Description Module membership
VNG0132C hypothetical protein VNG0132C 255
VNG0133G rpa replication factor A 255
VNG0361C hypothetical protein VNG0361C 255
VNG0405C hypothetical protein VNG0405C 296
VNG0426G rpoM DNA-directed RNA-polymerase subunit M 192, 296
VNG0439C hypothetical protein VNG0439C 255
VNG0865C hypothetical protein VNG0865C 253, 296
VNG0896G cda cytidine deaminase 255
VNG0905G pmu2 phosphomannomutase 255
VNG1297C S-adenosylmethionine synthetase 255
VNG1356G fumC fumarate hydratase 255
VNG1367G srp19 signal recognition particle 255
VNG1377G asnC transcription regulator 255, 296
VNG1379G suhB hypothetical protein VNG1379G 192, 296
VNG1442G htr12 Htr12 255
VNG1493G purF hypothetical protein VNG1493G 255
VNG1874C hypothetical protein VNG1874C 255
VNG1877C hypothetical protein VNG1877C 255
VNG1999H hypothetical protein VNG1999H 255
VNG2010G rps19e 30S ribosomal protein S19e 255
VNG2015C pyrH uridylate kinase 255, 296
VNG2017G lysS hypothetical protein VNG2017G 154, 296
VNG2021C hypothetical protein VNG2021C 255
VNG2072G serS seryl-tRNA synthetase 255
VNG2206G pmu1 phosphomannomutase 255
VNG2276G pmm phosphoglucomutase/phospho-mannomutase 255
VNG2331G uroM S-adenosyl-L-methionine:uroporphyrinogen III methyltransferase 88, 296
VNG2332G hemD uroporphyrinogen-III synthase 88, 296
VNG2333C hypothetical protein VNG2333C 255
VNG2504G pheS phenylalanyl-tRNA synthetase subunit alpha 255
VNG2515H hypothetical protein VNG2515H 88, 287, 296
VNG2576H hypothetical protein VNG2576H 259, 296
VNG2598G hisH1 glutamine amidotransferase subunit PdxT 255
VNG2643H hypothetical protein VNG2643H 255, 275
VNG6260G ftsZ5 cell division protein 255
VNG6268C hypothetical protein VNG6268C 255, 294
VNG6420H hypothetical protein VNG6420H 255
VNG7006 hypothetical protein VNG7006 255
VNG7007 hypothetical protein VNG7007 255
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 VNG1377G
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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