Organism : Halobacterium salinarum NRC-1 | Module List :
VNG0374G nusG

transcription antitermination protein NusG

CircVis
Functional Annotations (4)
Function System
Transcription antiterminator cog/ cog
transcription elongation regulator activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
L26e_arch tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG0374G
(Mouseover regulator name to see its description)

Warning: No Regulators were found for VNG0374G!

Warning: VNG0374G 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
1439 1.10e+00 tgCtgGtagtcGaacTcCtCG
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1440 1.80e+02 tTCa.CgcgtcgaACg.cgaCC.c
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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 VNG0374G

VNG0374G is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcription antiterminator cog/ cog
transcription elongation regulator activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
L26e_arch tigr/ tigrfam
Module neighborhood information for VNG0374G

VNG0374G has total of 30 gene neighbors in modules 253
Gene neighbors (30)
Gene Common Name Description Module membership
VNG0049H hypothetical protein VNG0049H 192, 253
VNG0089G pimT1 L-isoaspartyl protein carboxyl methyltransferase 253
VNG0156C hypothetical protein VNG0156C 253
VNG0274C hypothetical protein VNG0274C 253
VNG0327G gadD L-tyrosine decarboxylase 253, 270
VNG0374G nusG transcription antitermination protein NusG 253
VNG0481G mcmA1 methylmalonyl-CoA mutase subunit alpha 253
VNG0546C hypothetical protein VNG0546C 253
VNG0660H hypothetical protein VNG0660H 253
VNG0667G trp4 ABC transporter ATP-binding protein 253
VNG0769H hypothetical protein VNG0769H 253
VNG0860G rpoL DNA-directed RNA polymerase subunit L 253
VNG0865C hypothetical protein VNG0865C 253, 296
VNG0867G asnA asparagine synthetase 253
VNG0943C hypothetical protein VNG0943C 253, 284
VNG1110C hypothetical protein VNG1110C 253
VNG1262G eif2b translation initiation factor IF-2 subunit beta 253
VNG1486H hypothetical protein VNG1486H 253
VNG1487H hypothetical protein VNG1487H 253
VNG1591H hypothetical protein VNG1591H 253
VNG1727G cmk cytidylate kinase 253
VNG1766C hypothetical protein VNG1766C 253
VNG1782C hypothetical protein VNG1782C 253
VNG2045G gcp O-sialoglycoprotein endopeptidase/protein kinase 253
VNG2047G rps27ae 30S ribosomal protein S27ae 253
VNG2397G cysA hypothetical protein VNG2397G 253
VNG2577C hypothetical protein VNG2577C 253
VNG5050H predicted transcriptional regulator; PFAM03551:PadR/MarR family of transcriptional repressors; COG1695:predicted transcriptional regulators (PET=28) 253
VNG5173H None 253
VNG7069 hypothetical protein VNG7069 253
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 VNG0374G
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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