Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0679

sigma-54 dependent transcriptional regulator/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 DVU0679
(Mouseover regulator name to see its description)

DVU0679 is regulated by 17 influences and regulates 31 modules.
Regulators for DVU0679 (17)
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
DVU0309
DVU0749
315 combiner
DVU1144 315 tf
DVU1759 315 tf
DVU1760
DVU1340
315 combiner
DVU2378 315 tf
DVU2675 315 tf
DVU3111 315 tf
DVU3111
DVU2802
315 combiner
DVU3313 315 tf

Warning: DVU0679 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
601 1.40e-01 ttccgGCCcTTTC
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RegPredict
602 3.40e+04 TG.TgTCCTgT
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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 DVU0679

DVU0679 is enriched for 9 functions in 3 categories.
Module neighborhood information for DVU0679

DVU0679 has total of 51 gene neighbors in modules 291, 315
Gene neighbors (51)
Gene Common Name Description Module membership
DVU0022 HAMP domain/GGDEF domain/EAL domain-containing protein 15, 291
DVU0098 potA putrescine/spermidine ABC transporter ATPase protein 68, 315
DVU0364 pabA para-aminobenzoate/anthranilate synthase glutamine amidotransferase 116, 291
DVU0440 hypothetical protein DVU0440 82, 315
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
DVU0707 dctP TRAP transporter solute receptor DctP 92, 315
DVU0730 hypothetical protein DVU0730 30, 315
DVU0733 hypothetical protein DVU0733 89, 291
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
DVU0934 hypothetical protein DVU0934 296, 315
DVU1170 hypothetical protein DVU1170 216, 315
DVU1352 6-pyruvoyl tetrahydrobiopterin synthase 65, 291
DVU1386 hypothetical protein DVU1386 258, 291
DVU1403 cobO cob(I)alamin adenosyltransferase 86, 291
DVU1728 hypothetical protein DVU1728 137, 315
DVU1787 nuclease domain-containing protein 127, 315
DVU1960 cheA-2 chemotaxis protein CheA 311, 315
DVU1999 sulfate transporter family protein 175, 291
DVU2036 CopG family transcriptinal regulator 291, 336
DVU2131 hypothetical protein DVU2131 12, 291
DVU2307 C4-type zinc finger DksA/TraR family protein 26, 315
DVU2314 hypothetical protein DVU2314 260, 291
DVU2331 Smr family protein 137, 291
DVU2365 hypothetical protein DVU2365 304, 315
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
DVU2797 ferredoxin 139, 315
DVU2934 sigma-54 dependent transcriptional regulator/response regulator 198, 291
DVU3051 mutT mutator mutT protein 221, 291
DVU3099 tolQ-2 tolQ protein 44, 315
DVU3102 hypothetical protein DVU3102 54, 315
DVU3112 hypothetical protein 249, 315
DVU3114 kdsB 3-deoxy-manno-octulosonate cytidylyltransferase 25, 315
DVU3166 alanyl-tRNA synthetase family protein 315, 316
DVU3237 phosphoenolpyruvate synthase-like protein 160, 291
DVU3252 hypothetical protein DVU3252 116, 315
DVU3363 sun sun protein 96, 291
DVU3369 hypothetical protein DVU3369 185, 315
DVUA0095 hypothetical protein DVUA0095 153, 315
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 DVU0679
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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