Organism : Halobacterium salinarum NRC-1 | Module List :
VNG0530G troR

hypothetical protein VNG0530G

CircVis
Functional Annotations (4)
Function System
Mn-dependent transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
iron ion binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG0530G
(Mouseover regulator name to see its description)

VNG0530G is regulated by 7 influences and regulates 2 modules.
Regulators for VNG0530G troR (7)
Regulator Module Operator
VNG1510C 259 tf
VNG1510C
VNG6288C
259 combiner
VNG1616C 259 tf
VNG0511H 282 tf
VNG1510C 282 tf
VNG2112C 282 tf
VNG5068G
VNG1886C
282 combiner

Warning: VNG0530G 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
1451 1.10e+03 aaCccgGtGgTtTcg
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1452 1.10e+03 gGtTTtTGcGGggtggCCG
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1493 3.00e+00 GTGa.gacACgTGCcAGgacacGT
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1494 8.00e+02 cCGaaaAC
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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 VNG0530G

VNG0530G is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Mn-dependent transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
iron ion binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for VNG0530G

VNG0530G has total of 56 gene neighbors in modules 259, 282
Gene neighbors (56)
Gene Common Name Description Module membership
VNG0015H hypothetical protein VNG0015H 259, 268
VNG0021H hypothetical protein VNG0021H 251, 282
VNG0063G galE2 UDP-glucose 4-epimerase 164, 280, 282
VNG0127C hypothetical protein VNG0127C 282
VNG0137G cca tRNA CCA-pyrophosphorylase 259, 268
VNG0150H hypothetical protein VNG0150H 259, 270
VNG0378C hypothetical protein VNG0378C 118, 282
VNG0421C hypothetical protein VNG0421C 259, 274
VNG0468C hypothetical protein VNG0468C 259, 282
VNG0530G troR hypothetical protein VNG0530G 259, 282
VNG0544H hypothetical protein VNG0544H 282
VNG0555C hypothetical protein VNG0555C 190, 282
VNG0556G sgb succinoglycan biosynthesis transport protein 282
VNG0594H hypothetical protein VNG0594H 259, 282
VNG0600C hypothetical protein VNG0600C 88, 282
VNG0615C hypothetical protein VNG0615C 282
VNG0668C hypothetical protein VNG0668C 173, 282
VNG0669H hypothetical protein VNG0669H 259
VNG0707C hypothetical protein VNG0707C 282
VNG0733H hypothetical protein VNG0733H 259
VNG0845C hypothetical protein VNG0845C 185, 282
VNG0846C hypothetical protein VNG0846C 251, 282
VNG0862G hisF imidazole glycerol phosphate synthase subunit HisF 259
VNG0881G lig DNA ligase 172, 282
VNG0882Gm PHO2 p-nitrophenyl phosphatase 27, 274, 282
VNG0916G ark adaptive-response sensory-kinase 27, 274, 282
VNG0930G yvbT alkanal monooxygenase-like protein 265, 282
VNG1005H hypothetical protein VNG1005H 251, 282
VNG1035C hypothetical protein VNG1035C 129, 282
VNG1062G rfbQ rhamnosyl transferase 251, 282
VNG1070Gm gpdA1 glycerol-3-phosphate dehydrogenase chain A 252, 282
VNG1075G menA 1,4-dihydroxy-2-naphthoate octaprenyltransferase 259, 282
VNG1119H hypothetical protein VNG1119H 259, 284
VNG1145G mvk mevalonate kinase 259
VNG1151H hypothetical protein VNG1151H 251, 282
VNG1156G hsp3 Hsp3 178, 282
VNG1162H hypothetical protein VNG1162H 116, 282
VNG1329H hypothetical protein VNG1329H 259
VNG1344G dchpS DchpS 259
VNG1530H hypothetical protein VNG1530H 259
VNG1640H hypothetical protein VNG1640H 259, 300
VNG1673G pyrF hypothetical protein VNG1673G 259
VNG1771C hypothetical protein VNG1771C 259
VNG1905C hypothetical protein VNG1905C 259
VNG1937C cofG FO synthase subunit 1 259
VNG2012C hypothetical protein VNG2012C 257, 259
VNG2088G trm1 N2,N2-dimethylguanosine tRNA methyltransferase 259
VNG2158G oxrA putative oxidoreductase 259
VNG2254C DNA primase large subunit 259
VNG2461H hypothetical protein VNG2461H 282
VNG2576H hypothetical protein VNG2576H 259, 296
VNG2595G gbp4 GTP-binding protein 259
VNG2602G arsB hypothetical protein VNG2602G 259
VNG2614H hypothetical protein VNG2614H 259
VNG2622H hypothetical protein VNG2622H 259
VNG7132 hypothetical protein VNG7132 282
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 VNG0530G
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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