Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0749

DNA-binding response regulator

CircVis
Functional Annotations (4)
Function System
Response regulator of the LytR/AlgR family cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0749
(Mouseover regulator name to see its description)

DVU0749 is regulated by 21 influences and regulates 14 modules.
Regulators for DVU0749 (21)
Regulator Module Operator
DVU0030 26 tf
DVU0030
DVU3142
26 combiner
DVU0854 26 tf
DVU0854
DVU3167
26 combiner
DVU1063 26 tf
DVU1561 26 tf
DVU1561
DVU0749
26 combiner
DVU2275 26 tf
DVU2547
DVU2675
26 combiner
DVU2557 26 tf
DVU3167
DVU2909
26 combiner
DVU1645
DVU3193
304 combiner
DVU1674
DVU3095
304 combiner
DVU1674
DVU3186
304 combiner
DVU2319 304 tf
DVU2547
DVU2934
304 combiner
DVU2644 304 tf
DVU2644
DVU2799
304 combiner
DVU2934
DVU0621
304 combiner
DVU3084 304 tf
DVU3193
DVU2114
304 combiner

Warning: DVU0749 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
51 5.10e+01 TggCAAcGt
Loader icon
RegPredict
52 2.90e+02 Ccc.gCgtCaTGcCg
Loader icon
RegPredict
581 5.20e+04 TcCATGTCacA
Loader icon
RegPredict
582 2.00e+04 CggaTGCCCTG
Loader icon
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 DVU0749

DVU0749 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Response regulator of the LytR/AlgR family cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for DVU0749

DVU0749 has total of 51 gene neighbors in modules 26, 304
Gene neighbors (51)
Gene Common Name Description Module membership
DVU0051 hypothetical protein DVU0051 26, 46
DVU0055 ispH hydroxymethylbutenyl pyrophosphate reductase 185, 304
DVU0125 hypothetical protein DVU0125 26, 109
DVU0179 fused molybdenum-pterin binding domain-containing protein/site-specific recombinase phage integrase family 26, 320
DVU0187 GGDEF domain-containing protein 258, 304
DVU0244 hypothetical protein DVU0244 26, 269
DVU0245 protein phosphatase 46, 304
DVU0412 potassium uptake protein TrkA 46, 304
DVU0424 cls cardiolipin synthetase 26, 109
DVU0584 transposase 105, 304
DVU0611 ABC transporter ATP-binding protein 26, 109
DVU0687 tungsten-containing aldehyde:ferredoxin oxidoreductase 82, 304
DVU0689 rnhA ribonuclease H 82, 304
DVU0749 DNA-binding response regulator 26, 304
DVU0766 transporter 26, 296
DVU0834 rnhB ribonuclease HII 26, 266
DVU0884 hypothetical protein DVU0884 26, 123
DVU0897 RNA modification protein 172, 304
DVU0898 hypothetical protein DVU0898 172, 304
DVU0900 gmk guanylate kinase 172, 304
DVU0901 pyrF orotidine 5`-phosphate decarboxylase 32, 304
DVU0922 cytochrome c family protein 304, 307
DVU0960 hypothetical protein DVU0960 26, 123
DVU0996 hypothetical protein DVU0996 304, 307
DVU1088 hypothetical protein DVU1088 26, 109
DVU1182 hypothetical protein DVU1182 26, 172
DVU1188 hypothetical protein DVU1188 211, 304
DVU1531 methyltransferase 26, 292
DVU1536 Slt family transglycosylase 12, 304
DVU1657 hypothetical protein DVU1657 26, 109
DVU1802 hypothetical protein DVU1802 26, 261
DVU1909 acpS 4'-phosphopantetheinyl transferase 26, 296
DVU2092 thiamine biosynthesis protein ThiF 161, 304
DVU2307 C4-type zinc finger DksA/TraR family protein 26, 315
DVU2337 M24/M37 family peptidase 26, 112
DVU2365 hypothetical protein DVU2365 304, 315
DVU2477 pstS phosphate ABC transporter periplasmic phosphate-binding protein PstS 211, 304
DVU2479 phosphate ABC transporter permease 211, 304
DVU2543 hydroxylamine reductase 153, 304
DVU2739 pyruvate phosphate dikinase PEP/pyruvate binding subunit 112, 304
DVU2749 cobL precorrin-6Y C5,15-methyltransferase (decarboxylating) 166, 304
DVU2782 hypothetical protein DVU2782 26, 146
DVU2886 AraC family transcriptional regulator 251, 304
DVU2936 hypothetical protein DVU2936 26, 109
DVU2947 anaerobic ribonucleoside triphosphate reductase 81, 304
DVU2961 hypothetical protein DVU2961 285, 304
DVU3010 aminotransferase 112, 304
DVU3158 vacJ lipoprotein 26, 145
DVU3229 fliA RNA polymerase sigma factor for flagellar operon FliA 251, 304
DVU3254 PDZ domain-containing protein 26, 123
DVUA0072 glycosyl transferase, group 1 family protein 255, 304
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 DVU0749
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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