Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0804

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 DVU0804
(Mouseover regulator name to see its description)

DVU0804 is regulated by 15 influences and regulates 23 modules.
Regulators for DVU0804 (15)
Regulator Module Operator
DVU0749
DVU3142
260 combiner
DVU2423
DVU0539
260 combiner
DVU2836
DVU2275
260 combiner
DVU2894
DVU0539
260 combiner
DVU3255
DVU2644
260 combiner
DVU1063 161 tf
DVU1402
DVU1340
161 combiner
DVU1690
DVUA0143
161 combiner
DVU2557 161 tf
DVU2557
DVU1156
161 combiner
DVU2633 161 tf
DVU2909
DVU1690
161 combiner
DVU2909
DVU2527
161 combiner
DVUA0143
DVU1745
161 combiner
DVUA0151
DVU0936
161 combiner

Warning: DVU0804 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
307 1.60e+03 tC.gcTGTCAtccCg
Loader icon
RegPredict
308 2.40e+04 aTGtgtcGc.CatGg
Loader icon
RegPredict
495 1.60e-01 AacCCCcgT.cagcAat.gta.aA
Loader icon
RegPredict
496 7.10e-01 TgatGCTGgCA
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 DVU0804

DVU0804 is enriched for 9 functions in 3 categories.
Module neighborhood information for DVU0804

DVU0804 has total of 41 gene neighbors in modules 161, 260
Gene neighbors (41)
Gene Common Name Description Module membership
DVU0011 TRAP transporter solute receptor DctP 238, 260
DVU0038 acyltransferase domain-containing protein 69, 161
DVU0071 dinP DNA polymerase IV 161, 162
DVU0089 hypothetical protein DVU0089 161, 245
DVU0213 hypothetical protein DVU0213 161, 314
DVU0332 hypothetical protein DVU0332 89, 161
DVU0391 hypothetical protein DVU0391 99, 161
DVU0435 hypothetical protein DVU0435 161, 238
DVU0455 hypothetical protein DVU0455 161, 179
DVU0485 hypothetical protein DVU0485 161, 277
DVU0685 phosphomannomutase 17, 260
DVU0737 sensory box histidine kinase 202, 260
DVU0738 ABC transporter substrate-binding protein 202, 260
DVU0739 hypothetical protein DVU0739 202, 260
DVU0765 hydroxypyruvate reductase 27, 260
DVU0804 sigma-54 dependent transcriptional regulator/response regulator 161, 260
DVU0971 molybdenum cofactor biosynthesis protein 17, 161
DVU1024 rluD/coaE ribosomal large subunit pseudouridine synthase D/dephospho-CoA kinase 202, 260
DVU1100 tail fiber protein 12, 161
DVU1159 hypothetical protein DVU1159 161, 175
DVU1160 urea transporter 161, 185
DVU1261 hypothetical protein DVU1261 82, 260
DVU1262 twitching motility protein PilT 260, 275
DVU1566 phosphoadenosine phosphosulfate reductase 161, 225
DVU1804 glycosyl transferase group 1 family protein 25, 260
DVU2092 thiamine biosynthesis protein ThiF 161, 304
DVU2123 hypothetical protein DVU2123 161, 321
DVU2124 hypothetical protein DVU2124 161, 321
DVU2314 hypothetical protein DVU2314 260, 291
DVU2361 hypothetical protein DVU2361 161, 198
DVU2393 None 144, 260
DVU2419 hypothetical protein DVU2419 211, 260
DVU2462 oligopeptide ABC transporter permease 17, 161
DVU2544 iron-sulfur cluster-binding protein 153, 161
DVU2587 sensor histidine kinase 225, 260
DVU2629 hypothetical protein DVU2629 161, 238
DVU2784 FMN-dependent family dehydrogenase 160, 260
DVU2834 hypothetical protein DVU2834 161, 245
DVU2950 None 107, 260
DVU3195 lipoprotein 161, 214
DVU3203 DNA polymerase III subunit delta' 161, 316
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 DVU0804
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