Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2114

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 DVU2114
(Mouseover regulator name to see its description)

DVU2114 is regulated by 25 influences and regulates 70 modules.
Regulators for DVU2114 (25)
Regulator Module Operator
DVU0269 246 tf
DVU0539 246 tf
DVU0629 246 tf
DVU0629
DVU1744
246 combiner
DVU0916 246 tf
DVU2106 246 tf
DVU2827 246 tf
DVU2836 246 tf
DVU2836
DVU1744
246 combiner
DVU3080 246 tf
DVU3186 246 tf
DVU3255 246 tf
DVUA0143 246 tf
DVU0309 187 tf
DVU0539 187 tf
DVU2633 187 tf
DVU2644
DVU0916
187 combiner
DVU2644
DVU2633
187 combiner
DVU2686
DVU3255
187 combiner
DVU2827 187 tf
DVU2836 187 tf
DVU3142
DVU0813
187 combiner
DVU3255 187 tf
DVUA0143 187 tf
DVUA0151 187 tf

Warning: DVU2114 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
357 1.10e+02 GCA.Ggtgg.gaAacgagtTga
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RegPredict
358 1.10e+03 TTCCTTgCGAt
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RegPredict
469 8.50e-03 GTaTGaAaAtaaagaTaTAagAgA
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RegPredict
470 4.90e+00 aAggctaTcaaAggAaacCATcAG
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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 DVU2114

DVU2114 is enriched for 9 functions in 3 categories.
Module neighborhood information for DVU2114

DVU2114 has total of 34 gene neighbors in modules 187, 246
Gene neighbors (34)
Gene Common Name Description Module membership
DVU0252 hypothetical protein DVU0252 8, 246
DVU0472 hypothetical protein DVU0472 8, 246
DVU0473 hypothetical protein DVU0473 8, 246
DVU0475 membrane protein , truncation 246, 290
DVU0553 hypothetical protein DVU0553 8, 246
DVU0630 hypothetical protein DVU0630 8, 246
DVU0669 hypothetical protein DVU0669 98, 187
DVU0670 exopolysaccharide production protein 154, 246
DVU1019 hypothetical protein DVU1019 48, 187
DVU1020 HD domain/sensory box protein 54, 187
DVU1351 MarC membrane protein 187, 288
DVU1361 lpxB lipid A disaccharide synthase 187, 268
DVU1479 hypothetical protein DVU1479 246, 331
DVU1480 hypothetical protein DVU1480 187, 233
DVU1533 miaA tRNA delta(2)-isopentenylpyrophosphate transferase 78, 187
DVU1646 arsC arsenate reductase 8, 246
DVU1688 1-acyl-sn-glycerol-3-phosphate acyltransferase 98, 187
DVU1706 None 233, 246
DVU1750 hypothetical protein DVU1750 121, 246
DVU1859 hypothetical protein DVU1859 187, 219
DVU1966 hypothetical protein DVU1966 187, 219
DVU1995 anti-anti-sigma factor 121, 246
DVU2114 sigma-54 dependent transcriptional regulator/response regulator 187, 246
DVU2128 hypothetical protein DVU2128 187, 283
DVU2392 CesT family type III secretion chaperone 187, 246
DVU2409 solute-binding family 3 protein 48, 187
DVU2569 peptidyl-prolyl cis-trans isomerase, FKBP-type 98, 187
DVU2717 hypothetical protein DVU2717 233, 246
DVU2725 hypothetical protein DVU2725 8, 246
DVU2726 None 8, 246
DVU3080 transcriptional regulator 8, 187
DVUA0017 hypothetical protein DVUA0017 159, 187
DVUA0067 hypothetical protein DVUA0067 121, 187
DVUA0068 hypothetical protein DVUA0068 163, 187
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 DVU2114
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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