Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1519

transcriptional regulator

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1519
(Mouseover regulator name to see its description)

DVU1519 is regulated by 22 influences and regulates 0 modules.
Regulators for DVU1519 (22)
Regulator Module Operator
DVU0629
DVU1690
159 combiner
DVU0916 159 tf
DVU0916
DVU1745
159 combiner
DVU0916
DVU2835
159 combiner
DVU1144 159 tf
DVU1584 159 tf
DVU1690
DVU2835
159 combiner
DVU2106 159 tf
DVU2114 159 tf
DVU2644
DVU0916
159 combiner
DVU2644
DVU2114
159 combiner
DVU3186
DVU2527
159 combiner
DVU0629 111 tf
DVU1690
DVU2835
111 combiner
DVU1745 111 tf
DVU2114 111 tf
DVU2527 111 tf
DVU2527
DVU0629
111 combiner
DVU2686 111 tf
DVU2686
DVUA0100
111 combiner
DVU2835 111 tf
DVU3186 111 tf

Warning: DVU1519 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
213 7.40e-04 tca.tctTctTTTca
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RegPredict
214 1.70e+01 AgAaAaaT
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RegPredict
303 7.00e+01 At.TTCattt.taa
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RegPredict
304 4.40e+01 GTgcaAgatGa
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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 DVU1519

Warning: No Functional annotations were found!

Module neighborhood information for DVU1519

DVU1519 has total of 25 gene neighbors in modules 111, 159
Gene neighbors (25)
Gene Common Name Description Module membership
DVU1509 hypothetical protein DVU1509 143, 159
DVU1510 hypothetical protein DVU1510 159, 290
DVU1519 transcriptional regulator 111, 159
DVU1520 hypothetical protein DVU1520 111, 233
DVU1521 hypothetical protein DVU1521 111, 233
DVU1692 hypothetical protein DVU1692 159, 190
DVU2000 hypothetical protein DVU2000 111, 263
DVU2006 hypothetical protein DVU2006 111, 290
DVU2007 nuclease 111, 263
DVU2105 hypothetical protein DVU2105 111, 290
DVU2106 sigma-54 dependent transcriptional regulator 111, 263
DVU2174 hypothetical protein DVU2174 111, 190
DVU2177 hypothetical protein DVU2177 111, 190
DVU2179 ISDvu2, transposase OrfA 159, 171
DVU2220 hypothetical protein DVU2220 159, 171
DVU2686 S24 family peptidase 159, 290
DVU2709 None 111, 233
DVU2836 hypothetical protein DVU2836 159, 290
DVU2837 hypothetical protein DVU2837 111, 290
DVU2838 hypothetical protein DVU2838 111, 290
DVU2839 hypothetical protein DVU2839 159, 290
DVU2840 hypothetical protein DVU2840 71, 111
DVUA0017 hypothetical protein DVUA0017 159, 187
DVUA0019 type II DNA modification methyltransferase 111, 233
DVUA0020 type II restriction endonuclease 111, 233
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 DVU1519
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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