Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2319

transcriptional regulator domain-containing protein

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2319
(Mouseover regulator name to see its description)

DVU2319 is regulated by 18 influences and regulates 19 modules.
Regulators for DVU2319 (18)
Regulator Module Operator
DVU0063 316 tf
DVU0936
DVU0529
316 combiner
DVU1144 316 tf
DVU1518
DVU0936
316 combiner
DVU1674
DVU0936
316 combiner
DVU1745 316 tf
DVU2359 316 tf
DVU2423
DVU0619
316 combiner
DVU2527
DVU2251
316 combiner
DVU0309
DVU3193
92 combiner
DVU0379 92 tf
DVU0525 92 tf
DVU0653
DVU2251
92 combiner
DVU1561 92 tf
DVU1645
DVU1518
92 combiner
DVU1645
DVU1561
92 combiner
DVU3167
DVU0309
92 combiner
DVU3167
DVU0569
92 combiner

Warning: DVU2319 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
179 1.00e-06 TGCaTctGcTtTCcTGTtgGA
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RegPredict
180 7.10e-05 AaGCGCAcAcaGTGCcaCATGgCA
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RegPredict
603 2.20e-02 GGcaggggTGAtGcgGca
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RegPredict
604 4.50e+02 aCtcCgCcccgagcAtGgGccaCA
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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 DVU2319

Warning: No Functional annotations were found!

Module neighborhood information for DVU2319

DVU2319 has total of 53 gene neighbors in modules 92, 316
Gene neighbors (53)
Gene Common Name Description Module membership
DVU0017 hypothetical protein DVU0017 92, 245
DVU0057 TetR family transcriptional regulator 5, 316
DVU0058 RND family efflux transporter MFP subunit 68, 316
DVU0059 AcrB/AcrD/AcrF family protein 185, 316
DVU0127 hypothetical protein DVU0127 162, 316
DVU0176 glycerophosphoryl diester phosphodiesterase family protein 30, 316
DVU0605 hypothetical protein DVU0605 92, 331
DVU0696 hypothetical protein DVU0696 92, 138
DVU0705 dctM TRAP transporter subunit DctM 92, 265
DVU0706 TRAP transporter subunit DctQ 68, 92
DVU0707 dctP TRAP transporter solute receptor DctP 92, 315
DVU0708 hypothetical protein DVU0708 92, 116
DVU0709 hypothetical protein DVU0709 12, 92
DVU0909 hypothetical protein DVU0909 92, 244
DVU0914 cobS cobalamin-5-phosphate synthase 92, 160
DVU1229 hypothetical protein DVU1229 92, 224
DVU1235 hypothetical protein DVU1235 92, 266
DVU1388 hypothetical protein DVU1388 92, 225
DVU1591 hypothetical protein DVU1591 92, 116
DVU1747 hypothetical protein DVU1747 92, 243
DVU1759 molybdenum-binding protein 92, 179
DVU1895 major facilitator superfamily protein 127, 316
DVU1994 hypothetical protein DVU1994 92, 224
DVU2002 hypothetical protein DVU2002 92, 266
DVU2080 None 185, 316
DVU2101 hypothetical protein DVU2101 92, 312
DVU2102 OMP85 family outer membrane protein 92, 266
DVU2103 iron-sulfur cluster-binding/ATPase 92, 245
DVU2148 hypothetical protein DVU2148 5, 316
DVU2199 hypothetical protein DVU2199 70, 92
DVU2219 hypothetical protein DVU2219 92, 224
DVU2301 lipoprotein 92, 261
DVU2319 transcriptional regulator domain-containing protein 92, 316
DVU2320 3-octaprenyl-4-hydroxybenzoate carboxy-lyase 9, 316
DVU2321 hypothetical protein DVU2321 238, 316
DVU2467 rnr ribonuclease R 4, 316
DVU2610 hypothetical protein DVU2610 238, 316
DVU2821 hypothetical protein DVU2821 185, 316
DVU2877 hypothetical protein DVU2877 265, 316
DVU2888 cobalt ABC transporter ATP-binding protein 316, 334
DVU2889 BioY family protein 30, 316
DVU2899 hypothetical protein DVU2899 141, 316
DVU2911 hemolysin A 92, 134
DVU3074 hypothetical protein DVU3074 185, 316
DVU3075 hypothetical protein DVU3075 245, 316
DVU3091 hypothetical protein DVU3091 185, 316
DVU3120 hypothetical protein DVU3120 92, 127
DVU3131 transcriptional regulator 92, 321
DVU3166 alanyl-tRNA synthetase family protein 315, 316
DVU3203 DNA polymerase III subunit delta' 161, 316
DVU3340 hypothetical protein DVU3340 92, 239
DVUA0059 hypothetical protein DVUA0059 200, 316
DVUA0144 hypothetical protein DVUA0144 68, 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 DVU2319
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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