Organism : Halobacterium salinarum NRC-1 | Module List :
VNG2291G cat

4-hydroxybutyrate CoA transferase

CircVis
Functional Annotations (5)
Function System
Acetyl-CoA hydrolase cog/ cog
catalytic activity go/ molecular_function
acetyl-CoA metabolic process go/ biological_process
citrate CoA-transferase activity go/ molecular_function
citrate lyase complex go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG2291G
(Mouseover regulator name to see its description)

VNG2291G is regulated by 16 influences and regulates 0 modules.
Regulators for VNG2291G cat (16)
Regulator Module Operator
VNG1510C
VNG6288C
105 combiner
VNG6143H 105 tf
VNG0826C
VNG1237C
104 combiner
VNG1179C 104 tf
VNG1510C
VNG6288C
104 combiner
VNG2112C 104 tf
VNG6143H 104 tf
VNG6143H 92 tf
VNG0160G
VNG6288C
95 combiner
VNG1510C
VNG6288C
95 combiner
VNG2112C 95 tf
VNG6143H 95 tf
VNG6438G
VNG0826C
95 combiner
VNG1510C 94 tf
VNG1510C
VNG6288C
94 combiner
VNG6143H 94 tf

Warning: VNG2291G Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 10 motifs predicted.

Motif Table (10)
Motif Id e-value Consensus Motif Logo
1159 4.90e-01 TAtgAAg.ATG
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1160 7.80e+00 gacactgAaAtTaa.cgt.Tt
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1163 1.10e-02 ttAaTTa.Cg.TGTgAatca
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1164 1.20e-02 AatAatG.accGagAaaA.ctAa
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1165 2.10e+03 AAaGaACTTTtATaA
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1166 1.80e+03 AAagTAtT
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1181 4.30e+02 A.TGaAaTTa
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1182 1.00e+02 AatAagaaTa
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1183 4.00e-04 ttTAtgAAGgAt
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1184 1.00e+00 AAaACAaGAtT
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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 VNG2291G

VNG2291G is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Acetyl-CoA hydrolase cog/ cog
catalytic activity go/ molecular_function
acetyl-CoA metabolic process go/ biological_process
citrate CoA-transferase activity go/ molecular_function
citrate lyase complex go/ cellular_component
Module neighborhood information for VNG2291G

VNG2291G has total of 23 gene neighbors in modules 92, 94, 95, 104, 105
Gene neighbors (23)
Gene Common Name Description Module membership
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
VNG0868H hypothetical protein VNG0868H 95, 212
VNG0869G tfbD transcription initiation factor IIB 18, 91, 95, 212
VNG1247G ybhF ABC-type transport protein 95, 285
VNG1365C hypothetical protein VNG1365C 103, 104, 214
VNG1370G btuC corrinoid ABC transporter permease 11, 95, 104
VNG1371Gm btuD corrinoid ABC transporter ATPase 95, 103, 104, 214
VNG1372C hypothetical protein VNG1372C 95, 104, 214
VNG1649G trpD anthranilate phosphoribosyltransferase 28, 30, 48, 64, 87, 92
VNG1890H hypothetical protein VNG1890H 18, 105, 167
VNG2123G nhaC2 Na+/H+ antiporter 94
VNG2285C hypothetical protein VNG2285C 95, 104
VNG2286G mamA methylaspartate mutase subunit S 94, 95, 104, 105
VNG2288G mamB methylaspartate mutase 94, 95, 104
VNG2289G mal methylaspartate ammonia-lyase 104
VNG2290G maoC1 monoamine oxidase regulatory-like 94, 95, 104
VNG2291G cat 4-hydroxybutyrate CoA transferase 92, 94, 95, 104, 105
VNG6297C hypothetical protein VNG6297C 105, 207
VNG6340H hypothetical protein VNG6340H 62, 92, 93, 94, 96, 102, 103, 104
VNG7056 hypothetical protein VNG7056 86, 105, 106, 186, 209, 232, 238, 243, 257, 298
VNG7058 hypothetical protein VNG7058 105
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 VNG2291G
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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