Organism : Halobacterium salinarum NRC-1 | Module List :
VNG0147C

hypothetical protein VNG0147C

CircVis
Functional Annotations (3)
Function System
Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG0147C
(Mouseover regulator name to see its description)

VNG0147C is regulated by 5 influences and regulates 9 modules.
Regulators for VNG0147C (5)
Regulator Module Operator
KO_1_VNG_VNG0716G 224 ef
VNG1510C 224 tf
VNG1510C 194 tf
VNG1616C 194 tf
VNG1843C 194 tf

Warning: VNG0147C 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
1343 1.70e-03 CGacggCGacCgcga
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1344 1.30e+03 TtttatccaCGtGttccGt
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1389 2.00e-06 aATTAAaAacT
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1390 1.30e+02 Gat.AGcgAcacaaacGTA.aaaa
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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 VNG0147C

VNG0147C is enriched for 3 functions in 3 categories.
Module neighborhood information for VNG0147C

VNG0147C has total of 36 gene neighbors in modules 194, 224
Gene neighbors (36)
Gene Common Name Description Module membership
VNG0005H hypothetical protein VNG0005H 194
VNG0009G graD2 glucose-1-phosphate thymidylyltransferase 194, 265
VNG0077H hypothetical protein VNG0077H 194
VNG0098G rimK RimK 194, 270
VNG0147C hypothetical protein VNG0147C 194, 224
VNG0148H hypothetical protein VNG0148H 41, 80, 171, 189, 196, 219, 224
VNG0149G zntA hypothetical protein VNG0149G 171, 189, 196, 219, 224
VNG0151C hypothetical protein VNG0151C 194, 270
VNG0294G pnm N-methyltransferase-like protein 194, 267
VNG0380G caa cation antiporter 194, 270
VNG0390G graD1 glucose-1-phosphate thymidylyltransferase 194
VNG0410G rfbU2 LPS biosynthesis protein 194, 270
VNG0417H hypothetical protein VNG0417H 194
VNG0441H hypothetical protein VNG0441H 194
VNG0472H hypothetical protein VNG0472H 194, 270
VNG0876G purM phosphoribosylaminoimidazole synthetase 194
VNG0920H hypothetical protein VNG0920H 194
VNG1099C hypothetical protein VNG1099C 194
VNG1202C hypothetical protein VNG1202C 194
VNG1383G rad3a helicase 194
VNG1608C hypothetical protein VNG1608C 194
VNG1910H hypothetical protein VNG1910H 194
VNG2067H hypothetical protein VNG2067H 194, 287
VNG2084G phnE transport protein 194
VNG2117C adenine phosphoribosyltransferase 194
VNG2204H hypothetical protein VNG2204H 194
VNG2208G trpS1 tryptophanyl-tRNA synthetase 194
VNG2314H hypothetical protein VNG2314H 194
VNG2395C hypothetical protein VNG2395C 194
VNG2456Cm ABC transporter permease 194
VNG2533G pyrC dihydroorotase 194
VNG2639G uae UDP-N-acetylglucosamine 2-epimerase 194
VNG6326G trp6 daunorubicin resistance ABC transporter ATP-binding protein 117, 201, 224
VNG7009 hypothetical protein VNG7009 224
VNG7010 hypothetical protein VNG7010 224
VNG7011 repH plasmid replication protein RepH 17, 18, 30, 107, 122, 224, 287
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 VNG0147C
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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