Organism : Halobacterium salinarum NRC-1 | Module List :
VNG0825C

hypothetical protein VNG0825C

CircVis
Functional Annotations (4)
Function System
Molybdopterin-guanine dinucleotide biosynthesis protein cog/ cog
GTP binding go/ molecular_function
Mo-molybdopterin cofactor biosynthetic process go/ biological_process
mobB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG0825C
(Mouseover regulator name to see its description)

VNG0825C is regulated by 15 influences and regulates 0 modules.
Regulators for VNG0825C (15)
Regulator Module Operator
VNG0247C 43 tf
VNG1179C 43 tf
VNG1237C 43 tf
VNG1510C 43 tf
VNG1548C 43 tf
VNG6143H 43 tf
VNG1237C 5 tf
VNG1548C 5 tf
VNG2112C 5 tf
VNG1237C 4 tf
VNG2112C 4 tf
VNG6143H 4 tf
VNG0247C 32 tf
VNG1237C 32 tf
VNG6143H 32 tf

Warning: VNG0825C Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 8 motifs predicted.

Motif Table (8)
Motif Id e-value Consensus Motif Logo
987 3.00e-03 aAaAc.Acg.cCtagctaaaatAa
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988 8.90e-01 GtCTTggGCGAaTaGAAAtCTTCt
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989 1.10e+02 aAAtatAaaa.agga.taat
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990 8.30e+02 cgtccgCGA.tcG.t
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1041 9.60e+00 acTc.tgatTaAcA
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1042 2.00e+01 AcAcAcacgAgAcTg.gattA
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1063 8.80e-01 AcgAAtaGCtgtcCg
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1064 1.80e+01 T.cacaAc.aCgC.caagTcAcaA
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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 VNG0825C

VNG0825C is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Molybdopterin-guanine dinucleotide biosynthesis protein cog/ cog
GTP binding go/ molecular_function
Mo-molybdopterin cofactor biosynthetic process go/ biological_process
mobB tigr/ tigrfam
Module neighborhood information for VNG0825C

VNG0825C has total of 42 gene neighbors in modules 4, 5, 32, 43
Gene neighbors (42)
Gene Common Name Description Module membership
VNG0030H hypothetical protein VNG0030H 32, 233, 239
VNG0031H hypothetical protein VNG0031H 32, 233, 239
VNG0032H hypothetical protein VNG0032H 32, 233, 239
VNG0181G lpl Lpl 32, 43
VNG0215C hypothetical protein VNG0215C 32, 92, 93, 94, 103, 104, 105
VNG0216H hypothetical protein VNG0216H 4, 13, 15, 20, 32, 43, 92, 93, 94, 103, 104, 105
VNG0217H hypothetical protein VNG0217H 13, 15, 20, 32, 43, 53, 92, 93, 94, 103, 105
VNG0429H hypothetical protein VNG0429H 43
VNG0573C hypothetical protein VNG0573C 4, 5, 26, 28
VNG0730C hypothetical protein VNG0730C 43
VNG0731H hypothetical protein VNG0731H 43, 53, 164
VNG0825C hypothetical protein VNG0825C 4, 5, 32, 43
VNG0883H hypothetical protein VNG0883H 5, 26
VNG0985H hypothetical protein VNG0985H 4, 5, 164
VNG1453H hypothetical protein VNG1453H 4, 28
VNG1457C hypothetical protein VNG1457C 5
VNG1520G mutY A/G specific adenine glycosylase, repair protein 4, 5, 53
VNG1589C hypothetical protein VNG1589C 4, 5, 8, 28, 69, 85, 204
VNG1622G rfcB replication factor C large subunit 5, 28, 53, 140
VNG1648G trpF hypothetical protein VNG1648G 4, 5, 28, 30, 48, 64, 87
VNG1650H hypothetical protein VNG1650H 4, 5, 30, 34, 35, 245, 295
VNG1982C putative pseudouridylate synthase 43
VNG2096G cctB thermosome subunit beta 4, 5, 28, 53, 140, 173
VNG2100G iluA threonine dehydratase 5, 20, 26, 28
VNG2454C hypothetical protein VNG2454C 32
VNG6143H hypothetical protein VNG6143H 5, 26, 31, 72, 86, 106, 204, 232, 243, 295, 298
VNG6144G trsE transfer complex protein 4, 5, 42, 68, 295
VNG6150G orc1 orc / cell division control protein 6 4, 13, 38, 142, 189
VNG6152H hypothetical protein VNG6152H 4, 13, 15, 26, 31, 37, 142, 189, 272, 281, 297
VNG6170H hypothetical protein VNG6170H 4, 5, 15, 26, 28, 31, 36, 53, 60, 63, 69, 72, 85, 122
VNG6175G trkA2 TRK potassium uptake system protein 5, 15, 62, 69, 72, 177
VNG6176G kdpA potassium-transporting ATPase subunit A 5, 15, 18, 21, 26, 28, 31, 47, 51, 53, 62, 63, 69, 70, 72, 74, 177, 279
VNG6177G kdpB potassium-transporting ATPase subunit B 5, 15, 62, 63, 69, 72
VNG6178G kdpC potassium-transporting ATPase C chain 5, 15, 18, 26, 28, 31, 47, 51, 53, 62, 63, 69, 70, 72, 74, 177, 279
VNG6193H hypothetical protein VNG6193H 17, 32, 34, 38, 41, 42, 44, 80
VNG6230G gvpK2 GvpK protein, cluster B 4, 5, 8, 22, 28, 31, 141, 148, 181, 182, 188, 200
VNG6232G gvpJ2 GvpJ protein, cluster B 4, 5, 8, 28, 31, 42, 141, 148, 182, 188
VNG6239G gvpE2 GvpE protein, cluster B 4, 5, 8, 28, 141, 148, 182, 188, 200
VNG6244G gvpN2 GvpN protein, cluster B 5, 26, 53, 185
VNG6390H hypothetical protein VNG6390H 4, 26, 30, 34, 35, 245, 295
VNG6406H hypothetical protein VNG6406H 5, 127
VNG7109 hypothetical protein VNG7109 4, 18, 38, 91
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 VNG0825C
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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