Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVUA0057

sigma-54 dependent transcriptional regulator/response regulator

CircVis
Functional Annotations (10)
Function System
Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVUA0057
(Mouseover regulator name to see its description)

DVUA0057 is regulated by 19 influences and regulates 25 modules.
Regulators for DVUA0057 (19)
Regulator Module Operator
DVU0653
DVU2251
329 combiner
DVU1754 329 tf
DVU1754
DVU2785
329 combiner
DVU2690 329 tf
DVU2785
DVU0230
329 combiner
DVU2785
DVU2832
329 combiner
DVU2832 329 tf
DVU3334
DVU1967
329 combiner
DVUA0024 329 tf
DVUA0143 329 tf
DVU0230 200 tf
DVU0525 200 tf
DVU0653
DVU1690
200 combiner
DVU1967 200 tf
DVU2527
DVU2251
200 combiner
DVU2532 200 tf
DVU2644
DVU2114
200 combiner
DVU3186
DVU3095
200 combiner
DVUA0151 200 tf

Warning: DVUA0057 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.
Click on the RegPredict links to explore the motif in RegPredict.

Motif Table (4)
Motif Id e-value Consensus Motif Logo RegPredict
383 3.70e-02 CTTTTCAAGGAACCGAA
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RegPredict
384 3.00e+00 TCgcCttctCtgTC
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RegPredict
625 1.70e+04 ATggCgcAAgG
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RegPredict
626 8.70e+03 gCaTcgagCtT
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RegPredict
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 DVUA0057

DVUA0057 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
Module neighborhood information for DVUA0057

DVUA0057 has total of 30 gene neighbors in modules 200, 329
Gene neighbors (30)
Gene Common Name Description Module membership
DVU0086 hypothetical protein DVU0086 7, 200
DVU0181 modB molybdenum ABC transporter permease 284, 329
DVU0183 methyl-accepting chemotaxis protein 213, 329
DVU0283 AhpF family protein/thioredoxin reductase 284, 329
DVU0442 phoH-like protein 299, 329
DVU1416 hypothetical protein DVU1416 284, 329
DVU1698 hypothetical protein DVU1698 256, 329
DVU1714 hypothetical protein DVU1714 43, 329
DVU2271 pyruvate formate-lyase activating enzyme 97, 329
DVU2334 hypothetical protein DVU2334 284, 329
DVU2346 hypothetical protein DVU2346 284, 329
DVU2457 hypothetical protein DVU2457 200, 314
DVU2458 None 7, 200
DVU2540 2-hydroxyglutaryl-CoA dehydratase subunit D 165, 329
DVU2541 CoA-substrate-specific enzyme activase 43, 329
DVU2656 hypothetical protein DVU2656 326, 329
DVU3105 hypothetical protein DVU3105 7, 200
DVUA0040 polysaccharide biosynthesis protein 200, 328
DVUA0045 aminotransferase 200, 257
DVUA0047 hypothetical protein DVUA0047 61, 200
DVUA0048 exopolysaccharide production protein 200, 329
DVUA0055 hypothetical protein DVUA0055 200, 234
DVUA0057 sigma-54 dependent transcriptional regulator/response regulator 200, 329
DVUA0058 BNR/Asp-box repeat-containing protein 200, 340
DVUA0059 hypothetical protein DVUA0059 200, 316
DVUA0060 hypothetical protein DVUA0060 200, 340
DVUA0062 hypothetical protein DVUA0062 200, 257
DVUA0063 Orn/DAP/Arg family decarboxylase 200, 257
DVUA0141 hypothetical protein DVUA0141 7, 200
DVUA0146 hypothetical protein DVUA0146 61, 200
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 DVUA0057
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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