Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3334

sigma-54 dependent DNA-binding 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 DVU3334
(Mouseover regulator name to see its description)

DVU3334 is regulated by 18 influences and regulates 33 modules.
Regulators for DVU3334 (18)
Regulator Module Operator
DVU0230 106 tf
DVU0744
DVU2832
106 combiner
DVU1144 106 tf
DVU1754
DVU3305
106 combiner
DVU3080 106 tf
DVU3186
DVU3080
106 combiner
DVU3305
DVU1967
106 combiner
DVUA0151 106 tf
DVU0230
DVU1083
202 combiner
DVU0804
DVU3142
202 combiner
DVU1754 202 tf
DVU2588 202 tf
DVU2588
DVU1419
202 combiner
DVU2836 202 tf
DVU3142 202 tf
DVU3142
DVU1083
202 combiner
DVU3255
DVU0653
202 combiner
DVU3255
DVU1744
202 combiner

Warning: DVU3334 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
205 4.80e+00 catcAtcGtcatC.t
Loader icon
RegPredict
206 7.90e+00 TgTCtC.TCcAGc.Cgg.AAGcCg
Loader icon
RegPredict
387 1.00e+01 GTaGAACACTTCtgtgTtCTCGA
Loader icon
RegPredict
388 3.10e+01 GCAtCACCGtAcaGataTagC
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 DVU3334

DVU3334 is enriched for 9 functions in 3 categories.
Module neighborhood information for DVU3334

DVU3334 has total of 38 gene neighbors in modules 106, 202
Gene neighbors (38)
Gene Common Name Description Module membership
DVU0188 hypothetical protein DVU0188 106, 238
DVU0231 hypothetical protein DVU0231 99, 106
DVU0329 hypothetical protein DVU0329 106, 261
DVU0368 hypothetical protein DVU0368 68, 106
DVU0452 hypothetical protein DVU0452 106, 222
DVU0498 iron-sulfur cluster-binding protein 106, 202
DVU0628 buk butyrate kinase 86, 202
DVU0735 MOSC domain-containing protein 25, 202
DVU0737 sensory box histidine kinase 202, 260
DVU0738 ABC transporter substrate-binding protein 202, 260
DVU0739 hypothetical protein DVU0739 202, 260
DVU0747 ABC transporter ATP-binding protein 106, 144
DVU0750 methyl-accepting chemotaxis protein 106, 311
DVU0816 cobQ cobyric acid synthase 25, 202
DVU0878 dnaK suppressor protein 133, 202
DVU1024 rluD/coaE ribosomal large subunit pseudouridine synthase D/dephospho-CoA kinase 202, 260
DVU1034 hypothetical protein DVU1034 202, 326
DVU1153 hypothetical protein DVU1153 106, 289
DVU1297 hypothetical protein DVU1297 202, 326
DVU1385 hypothetical protein DVU1385 202, 203
DVU1431 hpt domain-containing protein/STAS domain-containing protein 202, 203
DVU1836 tRNA nucleotidyltransferase 202, 203
DVU1885 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B 202, 326
DVU1955 hypothetical protein 86, 202
DVU2137 sucCD succinyl-CoA synthase, beta/subunit alphas 106, 265
DVU2193 hypothetical protein DVU2193 106, 108
DVU2295 methyl-accepting chemotaxis protein 202, 203
DVU2591 tail fiber assembly protein 82, 106
DVU2592 hypothetical protein DVU2592 106, 256
DVU2668 glmU bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase 105, 106
DVU2872 lambda family phage portal protein 106, 278
DVU2873 hypothetical protein DVU2873 106, 107
DVU2887 hypothetical protein DVU2887 106, 251
DVU3058 sensory box histidine kinase/response regulator 82, 202
DVU3289 hypothetical protein DVU3289 106, 289
DVU3334 sigma-54 dependent DNA-binding response regulator 106, 202
DVU3390 None 106, 305
DVUA0129 cas3 CRISPR-associated helicase Cas3 domain-containing protein 202, 345
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 DVU3334
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