Organism : Halobacterium salinarum NRC-1 | Module List :
VNG2668G rpoH

DNA-directed RNA polymerase subunit H

CircVis
Functional Annotations (11)
Function System
DNA-directed RNA polymerase, subunit H, RpoH/RPB5 cog/ cog
DNA binding go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III activity go/ molecular_function
transcription, DNA-dependent go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG2668G
(Mouseover regulator name to see its description)

VNG2668G is regulated by 12 influences and regulates 0 modules.
Regulators for VNG2668G rpoH (12)
Regulator Module Operator
VNG1836G 197 tf
VNG5028G
VNG2243G
197 combiner
VNG0101G 110 tf
VNG2661G
VNG1029C
110 combiner
VNG2661G
VNG1483C
110 combiner
VNG0101G
VNG0320H
98 combiner
VNG0101G
VNG2163H
98 combiner
VNG0258H 98 tf
VNG1836G 98 tf
VNG2243G
VNG0293H
98 combiner
VNG0101G 40 tf
VNG2661G
VNG1029C
40 combiner

Warning: VNG2668G 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
1057 5.20e+02 CTTcAgcgCcT
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1058 6.80e+03 GTTTAT
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1171 4.90e+02 TaTggTTTCa
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1172 5.90e+02 AAcTaCG
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1193 1.30e+01 Gcaaagcg.aatgctTTtaa
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1194 5.40e+02 TctttTCgtcG
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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 VNG2668G

VNG2668G is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
DNA-directed RNA polymerase, subunit H, RpoH/RPB5 cog/ cog
DNA binding go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III activity go/ molecular_function
transcription, DNA-dependent go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
Module neighborhood information for VNG2668G

VNG2668G has total of 21 gene neighbors in modules 40, 98, 110, 197
Gene neighbors (21)
Gene Common Name Description Module membership
VNG0665G coxB1 cytochrome c oxidase subunit II 40, 283
VNG1001G guaB hypothetical protein VNG1001G 40, 242
VNG1768G eif5a translation initiation factor IF-5A 23, 24, 40, 59
VNG1774G hemA glutamyl-tRNA reductase 110, 137
VNG1873G icd hypothetical protein VNG1873G 110
VNG2293G fer2 ferredoxin 3, 110, 113
VNG2648G rps10p 30S ribosomal protein S10P 2, 3, 16, 23, 24, 29, 40, 110
VNG2649G eef1a elongation factor 1-alpha 2, 3, 16, 24, 29, 40, 79, 110
VNG2654Gm EEF2 elongation factor EF-2 2, 23, 110
VNG2657G rps7p 30S ribosomal protein S7P 98, 137
VNG2658G rps12P 30S ribosomal protein S12P 23, 39, 40, 45, 98, 110, 137
VNG2661G nusA transcription elongation factor NusA-like protein 98
VNG2662G rpoC DNA-directed RNA polymerase subunit A'' 45, 98
VNG2664Gm rpoA1 DNA-directed RNA polymerase subunit A' 40, 98, 110
VNG2665G rpoB' DNA-directed RNA polymerase subunit B' 40, 98, 110, 197
VNG2666G rpoB'' DNA-directed RNA polymerase subunit beta'' 2, 16, 40, 98, 110
VNG2668G rpoH DNA-directed RNA polymerase subunit H 40, 98, 110, 197
VNG6199G cdc48d cell division cycle protein 98, 125, 240
VNG6201G hsp5 heat shock protease protein 3, 49, 71, 79, 98, 100, 113, 187, 240
VNG7024 gvpD gas vesicle protein GvpD 98
VNG7026 gvpC gas vesicle protein GvpC 98
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 VNG2668G
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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