Organism : Halobacterium salinarum NRC-1 | Module List :
VNG2384G nrdB1

ribonucleotide-diphosphate reductase alpha subunit

CircVis
Functional Annotations (12)
Function System
Ribonucleotide reductase, alpha subunit cog/ cog
nucleotide binding go/ molecular_function
ribonucleoside-diphosphate reductase activity go/ molecular_function
ribonucleoside-diphosphate reductase activity go/ molecular_function
protein binding go/ molecular_function
ribonucleoside-diphosphate reductase complex go/ cellular_component
DNA replication go/ biological_process
cobalamin binding go/ molecular_function
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
NrdJ_Z tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG2384G
(Mouseover regulator name to see its description)

VNG2384G is regulated by 3 influences and regulates 0 modules.
Regulators for VNG2384G nrdB1 (3)
Regulator Module Operator
VNG1237C 268 tf
VNG1510C 268 tf
VNG6143H 268 tf

Warning: VNG2384G 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
1469 1.60e+04 acgAaAtcC.ggT
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1470 3.30e+04 ATACAATCA
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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 VNG2384G

VNG2384G is enriched for 12 functions in 3 categories.
Enrichment Table (12)
Function System
Ribonucleotide reductase, alpha subunit cog/ cog
nucleotide binding go/ molecular_function
ribonucleoside-diphosphate reductase activity go/ molecular_function
ribonucleoside-diphosphate reductase activity go/ molecular_function
protein binding go/ molecular_function
ribonucleoside-diphosphate reductase complex go/ cellular_component
DNA replication go/ biological_process
cobalamin binding go/ molecular_function
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
NrdJ_Z tigr/ tigrfam
Module neighborhood information for VNG2384G

VNG2384G has total of 30 gene neighbors in modules 268
Gene neighbors (30)
Gene Common Name Description Module membership
VNG0015H hypothetical protein VNG0015H 259, 268
VNG0072H hypothetical protein VNG0072H 97, 268
VNG0121H hypothetical protein VNG0121H 117, 268
VNG0137G cca tRNA CCA-pyrophosphorylase 259, 268
VNG0154G merA mercury(II) reductase 116, 268
VNG0159G mutL DNA mismatch repair protein 251, 268
VNG0178H hypothetical protein VNG0178H 97, 268
VNG0222C hypothetical protein VNG0222C 262, 268
VNG0244H hypothetical protein VNG0244H 54, 268
VNG0251C hypothetical protein VNG0251C 241, 268
VNG0277G crtI3 phytoene dehydrogenase 254, 268
VNG0351C hypothetical protein VNG0351C 190, 268
VNG0354C hypothetical protein VNG0354C 268
VNG0363G nfi hypothetical protein VNG0363G 233, 268
VNG0365G arsA1 arsenical pump-driving ATPase 268
VNG0371G acd1 acyl-CoA dehydrogenase 111, 268
VNG0576C hypothetical protein VNG0576C 268
VNG0814C hypothetical protein VNG0814C 268
VNG1037G hpcE 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase 268
VNG1744H hypothetical protein VNG1744H 268
VNG1927H hypothetical protein VNG1927H 268
VNG2029H hypothetical protein VNG2029H 268
VNG2132Gm FER1 ferredoxin 268
VNG2238C hypothetical protein VNG2238C 268
VNG2274C hypothetical protein VNG2274C 268
VNG2384G nrdB1 ribonucleotide-diphosphate reductase alpha subunit 268
VNG6209H hypothetical protein VNG6209H 268
VNG6261G yocR sodium-dependent transporter 268
VNG7048 hypothetical protein VNG7048 268
VNG7122 hypothetical protein VNG7122 268
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 VNG2384G
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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