Organism : Halobacterium salinarum NRC-1 | Module List :
VNG0055H

hypothetical protein VNG0055H

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG0055H
(Mouseover regulator name to see its description)

VNG0055H is regulated by 14 influences and regulates 0 modules.
Regulators for VNG0055H (14)
Regulator Module Operator
VNG1179C 41 tf
VNG1237C 41 tf
VNG2112C 41 tf
VNG6143H 41 tf
VNG6389G 41 tf
VNG6438G 41 tf
VNG0869G 185 tf
VNG1510C 185 tf
VNG2112C 37 tf
VNG6143H 37 tf
VNG1179C 183 tf
VNG2579G 183 tf
VNG5163G 183 tf
VNG6389G 183 tf

Warning: VNG0055H 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
1051 7.00e-06 AaAtagatatgAttg.aataT
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1052 5.70e+01 AaGa.ATT
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1059 3.50e+01 AatttcTctTgcGGAagta
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1060 1.20e+04 CcacGAcgAaCgCC
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1321 2.50e+02 ATAACTGCaATA
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1322 9.30e+02 AA.CAgCAC
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1325 4.40e+02 TGATAAA
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1326 6.70e+02 AATGACaGTaACA
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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 VNG0055H

Warning: No Functional annotations were found!

Module neighborhood information for VNG0055H

VNG0055H has total of 31 gene neighbors in modules 37, 41, 183, 185
Gene neighbors (31)
Gene Common Name Description Module membership
VNG0055H hypothetical protein VNG0055H 37, 41, 183, 185
VNG0148H hypothetical protein VNG0148H 41, 80, 171, 189, 196, 219, 224
VNG0204H hypothetical protein VNG0204H 41
VNG0845C hypothetical protein VNG0845C 185, 282
VNG0993H hypothetical protein VNG0993H 37, 188
VNG1030G pgsA CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase 183
VNG1033G hisC1 histidinol-phosphate aminotransferase 183
VNG1064H hypothetical protein VNG1064H 17, 37, 96, 108
VNG1270H hypothetical protein VNG1270H 18, 30, 37, 42
VNG1271H hypothetical protein VNG1271H 18, 30, 37
VNG1525C hypothetical protein VNG1525C 41
VNG1534a birA biotin operon repressor and biotin-(acetyl-CoA carboxylase) ligase 41
VNG2034H hypothetical protein VNG2034H 41
VNG2185H hypothetical protein VNG2185H 41
VNG2632G yusZ2 oxidoreductase 34, 41, 143
VNG5120H None 18, 37, 198
VNG5157H None 37
VNG6005H hypothetical protein VNG6005H 37, 198
VNG6152H hypothetical protein VNG6152H 4, 13, 15, 26, 31, 37, 142, 189, 272, 281, 297
VNG6180H hypothetical protein VNG6180H 37
VNG6191H hypothetical protein VNG6191H 17, 30, 34, 38, 41, 44, 80, 91
VNG6193H hypothetical protein VNG6193H 17, 32, 34, 38, 41, 42, 44, 80
VNG6196G phoT2 sodium-dependent phosphate transporter 30, 36, 41, 80, 87, 89
VNG6242G gvpC2 GvpC protein, cluster B 42, 185
VNG6244G gvpN2 GvpN protein, cluster B 5, 26, 53, 185
VNG6327H hypothetical protein VNG6327H 41
VNG6344H hypothetical protein VNG6344H 17, 41
VNG6416H hypothetical protein VNG6416H 13, 15, 21, 41, 60, 281
VNG6418H hypothetical protein VNG6418H 13, 18, 21, 41, 60, 281
VNG7107 putative ISH4 transposase 37, 147
VNG7134 hypothetical protein VNG7134 183, 272
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 VNG0055H
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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