Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0110

sigma-54 dependent transcriptional regulator/response regulator

CircVis
Functional Annotations (9)
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
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 DVU0110
(Mouseover regulator name to see its description)

DVU0110 is regulated by 23 influences and regulates 46 modules.
Regulators for DVU0110 (23)
Regulator Module Operator
DVU0277
DVU0946
117 combiner
DVU0525 117 tf
DVU0653 117 tf
DVU0946 117 tf
DVU0946
DVU1760
117 combiner
DVU0946
DVU2956
117 combiner
DVU2788
DVU0946
117 combiner
DVU2832
DVU1745
117 combiner
DVU3023 117 tf
DVU3167 117 tf
DVU3167
DVU0916
117 combiner
DVU3186 117 tf
DVU3186
DVU0653
117 combiner
DVU0230
DVU1745
141 combiner
DVU0594 141 tf
DVU0653 141 tf
DVU0946 141 tf
DVU1517 141 tf
DVU1518
DVU1561
141 combiner
DVU2785
DVU0529
141 combiner
DVU2785
DVU1517
141 combiner
DVU2788
DVU0653
141 combiner
DVU3023
DVU2319
141 combiner

Warning: DVU0110 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
225 7.20e+00 cttgtcatcgctGTA
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RegPredict
226 1.30e+02 cgaTGCgctGccg.a.cggCt
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RegPredict
271 4.80e-03 AatTAAAcAAAaGccGaGaaACaC
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RegPredict
272 4.50e+00 GTatCgTgtgGgCtTgcgCcc
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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 DVU0110

DVU0110 is enriched for 9 functions in 3 categories.
Module neighborhood information for DVU0110

DVU0110 has total of 48 gene neighbors in modules 117, 141
Gene neighbors (48)
Gene Common Name Description Module membership
DVU0007 asnC asparaginyl-tRNA synthetase 35, 117
DVU0110 sigma-54 dependent transcriptional regulator/response regulator 117, 141
DVU0156 ATP-dependent DNA helicase UvrD 117, 141
DVU0326 hypE hydrogenase expression/formation protein HypE 117, 250
DVU0352 aminotransferase 141, 277
DVU0413 TrkH family potassium uptake protein 48, 117
DVU0612 STAS domain-containing protein 48, 117
DVU0633 penicillin-binding protein 141, 176
DVU0682 DNA-binding protein 141, 229
DVU0760 hypothetical protein DVU0760 35, 117
DVU0983 hypothetical protein DVU0983 35, 141
DVU1181 response regulator 141, 279
DVU1370 hypothetical protein DVU1370 9, 141
DVU1376 ilvB-2 acetolactate synthase large subunit, biosynthetic type 117, 303
DVU1461 hemA glutamyl-tRNA reductase 117, 334
DVU1462 cytochrome c assembly protein 117, 303
DVU1463 siroheme synthase 117, 334
DVU1464 heptosyltransferase family protein 117, 303
DVU1544 mechanosensitive ion channel family protein 117, 141
DVU1581 hypothetical protein DVU1581 141, 294
DVU1883 hypothetical protein DVU1883 117, 249
DVU2140 tmk thymidylate kinase 117, 268
DVU2302 glutathione-regulated potassium-efflux system protein KefB 141, 277
DVU2329 hypB hydrogenase accessory protein HypB 35, 117
DVU2330 MRP family protein 35, 141
DVU2338 HhH-GPD family DNA repair protein 117, 141
DVU2413 radical SAM domain-containing protein 141, 185
DVU2425 rarD rarD protein 141, 195
DVU2463 recN DNA repair protein RecN 23, 141
DVU2491 ABC transporter ATP-binding protein 35, 117
DVU2581 response regulator 141, 278
DVU2765 metallo-beta-lactamase family protein 35, 117
DVU2766 hypothetical protein DVU2766 35, 117
DVU2767 iron-sulfur flavoprotein 35, 117
DVU2780 hypothetical protein DVU2780 69, 141
DVU2899 hypothetical protein DVU2899 141, 316
DVU2900 amidohydrolase family protein 83, 141
DVU2901 pyrB aspartate carbamoyltransferase catalytic subunit 141, 344
DVU2902 pyrC dihydroorotase 141, 278
DVU2932 hypothetical protein DVU2932 117, 141
DVU3009 radical SAM domain-containing protein 117, 176
DVU3067 hypF [NiFe] hydrogenase maturation protein HypF [Desulfovibrio vulgaris str. Hildenborough] 35, 117
DVU3086 cobB-2 cobyrinic acid a,c-diamide synthase 83, 141
DVU3087 cobH precorrin-8X methylmutase 46, 141
DVU3097 outer membrane efflux protein 141, 249
DVU3172 hypothetical protein DVU3172 35, 117
DVU3216 sensor histidine kinase 117, 141
DVU3278 peptidase/PDZ domain-containing protein 83, 141
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 DVU0110
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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