Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0230

transcriptional regulator cII

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0230
(Mouseover regulator name to see its description)

DVU0230 is regulated by 24 influences and regulates 123 modules.
Regulators for DVU0230 (24)
Regulator Module Operator
DVU0030 156 tf
DVU0529 156 tf
DVU1517 156 tf
DVU1645
DVU1730
156 combiner
DVU1730 156 tf
DVU2036
DVU2582
156 combiner
DVU2423 156 tf
DVU2832 156 tf
DVU3255
DVU0653
156 combiner
DVU3255
DVU2934
156 combiner
DVUA0151 156 tf
DVU0529
DVU0525
3 combiner
DVU0653 3 tf
DVU1517 3 tf
DVU1561
DVU0525
3 combiner
DVU1561
DVUA0024
3 combiner
DVU1754 3 tf
DVU2086
DVU1517
3 combiner
DVU2195 3 tf
DVU2532
DVU0110
3 combiner
DVU2532
DVU0653
3 combiner
DVU2832 3 tf
DVU3142 3 tf
DVU3167 3 tf

Warning: DVU0230 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
5 4.80e+02 aat.gaTcaC.gAAAGaAAga
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RegPredict
6 2.30e+03 tCgaGcgtgaaCcC.ACgCC
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RegPredict
297 2.20e-03 aTtTttatATgattttcaagaaa
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RegPredict
298 2.20e-01 AtattGcctgtaaa..ttGttTaC
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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 DVU0230

Warning: No Functional annotations were found!

Module neighborhood information for DVU0230

DVU0230 has total of 35 gene neighbors in modules 3, 156
Gene neighbors (35)
Gene Common Name Description Module membership
DVU0223 hypothetical protein DVU0223 90, 156
DVU0224 hypothetical protein DVU0224 94, 156
DVU0230 transcriptional regulator cII 3, 156
DVU0426 chromate transport family protein 3, 32
DVU1482 hypothetical protein DVU1482 3, 100
DVU1491 hypothetical protein DVU1491 134, 156
DVU1492 None 90, 156
DVU1641 hypothetical protein DVU1641 156, 289
DVU1642 hypothetical protein DVU1642 156, 289
DVU1674 transcriptional regulator 156, 157
DVU1675 hypothetical protein DVU1675 156, 157
DVU1699 hypothetical protein DVU1699 3, 256
DVU1738 phage integrase family site specific recombinase 100, 156
DVU1957 hypothetical protein DVU1957 3, 193
DVU1971 hypothetical protein DVU1971 156, 179
DVU2008 hypothetical protein DVU2008 100, 156
DVU2158 hypothetical protein DVU2158 3, 72
DVU2197 phage integrase family site specific recombinase 25, 156
DVU2249 hypothetical protein DVU2249 3, 244
DVU2296 mtgA monofunctional biosynthetic peptidoglycan transglycosylase 3, 244
DVU2343 amino acid ABC transporter ATP-binding protein 3, 28
DVU2432 sensory box protein 3, 295
DVU2567 hypothetical protein DVU2567 3, 270
DVU2741 livG high-affinity branched chain amino acid ABC transporter ATP-binding protein 2, 156
DVU2742 livM high-affinity branched chain amino acid ABC transporter permease 156, 289
DVU2744 high-affinity branched-chain amino acid ABC transporter perisplasmic amino acid binding protein 156, 289
DVU2986 pspC phage shock protein C 13, 156
DVU2987 hypothetical protein DVU2987 13, 156
DVU2988 pspA phage shock protein A 13, 156
DVU3078 hypothetical protein DVU3078 3, 85
DVU3249 lipoprotein 3, 295
DVU3251 HPP family membrane protein 3, 264
DVU3311 hypothetical protein DVU3311 156, 313
DVUA0046 glycosyl transferase, group 2 family protein 3, 61
DVUA0084 AbrB family transcriptional regulator 156, 289
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 DVU0230
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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