Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2036

CopG family transcriptinal regulator

CircVis
Functional Annotations (3)
Function System
Predicted transcriptional regulator cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2036
(Mouseover regulator name to see its description)

DVU2036 is regulated by 22 influences and regulates 45 modules.
Regulators for DVU2036 (22)
Regulator Module Operator
DVU0379
DVU1949
291 combiner
DVU2086
DVU2251
291 combiner
DVU2788
DVU2086
291 combiner
DVU3066 291 tf
DVU3193
DVU0230
291 combiner
DVU3193
DVU2819
291 combiner
DVU3193
DVU2832
291 combiner
DVUA0100
DVU1949
291 combiner
DVU0606
DVU3255
336 combiner
DVU0682
DVU3255
336 combiner
DVU1584
DVU3023
336 combiner
DVU1754 336 tf
DVU2086 336 tf
DVU2423
DVU2588
336 combiner
DVU2588
DVU3381
336 combiner
DVU2836 336 tf
DVU3023 336 tf
DVU3142
DVU0813
336 combiner
DVU3142
DVU1419
336 combiner
DVU3255
DVU0594
336 combiner
DVU3255
DVU1744
336 combiner
DVUA0151 336 tf

Warning: DVU2036 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
557 2.20e+02 TgcCgTtgtCgcccggcCcGtgTt
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RegPredict
558 8.90e+03 tTTcCATgTgaAtC
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RegPredict
637 9.50e+02 AtcGtGctTTc
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RegPredict
638 6.60e+02 tTcTaTgttTtcaatttAT
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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 DVU2036

DVU2036 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Predicted transcriptional regulator cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for DVU2036

DVU2036 has total of 46 gene neighbors in modules 291, 336
Gene neighbors (46)
Gene Common Name Description Module membership
DVU0022 HAMP domain/GGDEF domain/EAL domain-containing protein 15, 291
DVU0364 pabA para-aminobenzoate/anthranilate synthase glutamine amidotransferase 116, 291
DVU0506 DHH family protein 163, 336
DVU0614 hypothetical protein DVU0614 205, 291
DVU0679 sigma-54 dependent transcriptional regulator/response regulator 291, 315
DVU0680 sensory box histidine kinase 14, 291
DVU0681 sensor histidine kinase/response regulator 15, 291
DVU0733 hypothetical protein DVU0733 89, 291
DVU0787 hypothetical protein DVU0787 75, 336
DVU0788 mreC rod shape-determining protein MreC 300, 336
DVU0826 glycolate oxidase, iron-sulfur subunit 82, 291
DVU0827 glycolate oxidase subunit GlcD 166, 291
DVU0828 smpB SsrA-binding protein 166, 291
DVU0829 ptsI phosphoenolpyruvate-protein phosphotransferase 82, 291
DVU0890 hom homoserine dehydrogenase 32, 291
DVU0905 lipA lipoyl synthase 54, 291
DVU0924 rumA 23S rRNA (uracil-5-)-methyltransferase RumA 216, 291
DVU0933 response regulator 291, 315
DVU0967 His/Glu/Gln/Arg/opine ABC transporter permease 154, 336
DVU0968 amino acid ABC transporter ATP-binding protein 336, 344
DVU1352 6-pyruvoyl tetrahydrobiopterin synthase 65, 291
DVU1386 hypothetical protein DVU1386 258, 291
DVU1403 cobO cob(I)alamin adenosyltransferase 86, 291
DVU1532 coaD phosphopantetheine adenylyltransferase 135, 336
DVU1671 ABC transporter ATP-binding protein/permease 154, 336
DVU1673 acyltransferase 282, 336
DVU1776 hypothetical protein DVU1776 126, 336
DVU1935 phosphonate ABC transporter permease 75, 336
DVU1999 sulfate transporter family protein 175, 291
DVU2036 CopG family transcriptinal regulator 291, 336
DVU2131 hypothetical protein DVU2131 12, 291
DVU2314 hypothetical protein DVU2314 260, 291
DVU2331 Smr family protein 137, 291
DVU2374 lolD lipoprotein releasing system, ATP-binding protein 237, 336
DVU2375 lipoprotein releasing system, permease 300, 336
DVU2433 hypothetical protein DVU2433 230, 291
DVU2525 hynB-2 periplasmic 77, 291
DVU2620 hypothetical protein DVU2620 150, 291
DVU2748 cobM precorrin-4 C11-methyltransferase 166, 291
DVU2934 sigma-54 dependent transcriptional regulator/response regulator 198, 291
DVU3051 mutT mutator mutT protein 221, 291
DVU3069 hypothetical protein DVU3069 237, 336
DVU3164 ABC transporter permease 174, 336
DVU3165 hypothetical protein DVU3165 75, 336
DVU3237 phosphoenolpyruvate synthase-like protein 160, 291
DVU3363 sun sun protein 96, 291
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 DVU2036
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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