Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2394

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 DVU2394
(Mouseover regulator name to see its description)

DVU2394 is regulated by 23 influences and regulates 18 modules.
Regulators for DVU2394 (23)
Regulator Module Operator
DVU0063
DVU0679
342 combiner
DVU0277
DVU1744
342 combiner
DVU0309
DVU1949
342 combiner
DVU0606 342 tf
DVU0679
DVU1730
342 combiner
DVU1949 342 tf
DVU1949
DVU1730
342 combiner
DVU2378 342 tf
DVU2378
DVU2251
342 combiner
DVU2378
DVU3080
342 combiner
DVU2675
DVU1744
342 combiner
DVUA0143 342 tf
DVUA0143
DVU1949
342 combiner
DVU0063 155 tf
DVU0277
DVU2378
155 combiner
DVU0594 155 tf
DVU0606 155 tf
DVU0679
DVU1949
155 combiner
DVU1949
DVU1730
155 combiner
DVU2378 155 tf
DVU2378
DVU0744
155 combiner
DVU2378
DVU3080
155 combiner
DVU2675
DVU1744
155 combiner

Warning: DVU2394 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
295 3.80e+02 GttgtggctCaTgaaG.tggt.t
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RegPredict
296 4.40e+03 ACgagaCagCAcg.CgCgGGcAt
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RegPredict
649 7.10e-04 CAagCggcgTCTGtacggctaaCG
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RegPredict
650 5.40e-01 tTtcaTcaagGTTtCAcGCatG
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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 DVU2394

DVU2394 is enriched for 9 functions in 3 categories.
Module neighborhood information for DVU2394

DVU2394 has total of 42 gene neighbors in modules 155, 342
Gene neighbors (42)
Gene Common Name Description Module membership
DVU0354 hypothetical protein DVU0354 155, 179
DVU0411 heptosyltransferase family protein 153, 342
DVU0547 high-affinity branched chain amino acid ABC transporter periplasmic branched chain amino acid-binding protein 255, 342
DVU1360 galE UDP-glucose 4-epimerase 37, 342
DVU1439 hypothetical protein DVU1439 87, 155
DVU1473 hypothetical protein DVU1473 155, 309
DVU1475 PhoU family protein 155, 175
DVU1815 cytochrome c oxidase subunit I 102, 155
DVU2067 GGDEF domain-containing protein 219, 342
DVU2068 HD domain-containing protein 121, 342
DVU2162 hypothetical protein DVU2162 155, 342
DVU2366 hypothetical protein DVU2366 69, 155
DVU2379 M16 family peptidase 155, 191
DVU2380 ABC transporter ATP-binding protein 155, 191
DVU2382 hypothetical protein DVU2382 155, 254
DVU2384 ABC transporter periplasmic substrate-binding protein 155, 342
DVU2385 ABC transporter permease 155, 342
DVU2386 ABC transporter permease 155, 342
DVU2387 ABC transporter ATP-binding protein 155, 342
DVU2388 tolQ-1 tolQ protein 155, 191
DVU2389 biopolymer ExbD/TolR family transporter 155, 191
DVU2390 TonB domain-containing protein 155, 191
DVU2394 sigma-54 dependent transcriptional regulator/response regulator 155, 342
DVU2395 sensor histidine kinase 155, 342
DVU2396 iron-containing alcohol dehydrogenase 155, 342
DVU2397 hypothetical protein DVU2397 155, 342
DVU2398 hypothetical protein DVU2398 155, 342
DVU2399 hydrogenase 155, 342
DVU2400 hydrogenase 155, 342
DVU2401 hydrogenase, iron-sulfur cluster-binding subunit 155, 342
DVU2402 hdrA heterodisulfide reductase subunit A 155, 342
DVU2403 hdrB heterodisulfide reductase subunit B 155, 342
DVU2404 hdrC heterodisulfide reductase subunit C 155, 342
DVU2405 iron-containing alcohol dehydrogenase 155, 342
DVU2406 hypothetical protein DVU2406 155, 342
DVU2453 hypothetical protein DVU2453 245, 342
DVU2454 hypothetical protein DVU2454 245, 342
DVU2455 NAD-dependent epimerase/dehydratase family protein 245, 342
DVU2459 hypothetical protein DVU2459 155, 342
DVU2498 hypothetical protein DVU2498 37, 342
DVU2551 HD domain-containing protein 37, 342
DVU2882 folC folylpolyglutamate synthase 155, 179
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 DVU2394
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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