Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2894

sigma-54 dependent transcriptional regulator

CircVis
Functional Annotations (7)
Function System
Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains cog/ cog
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 DVU2894
(Mouseover regulator name to see its description)

DVU2894 is regulated by 21 influences and regulates 9 modules.
Regulators for DVU2894 (21)
Regulator Module Operator
DVU1419 115 tf
DVU1547 115 tf
DVU1645 115 tf
DVU2275 115 tf
DVU2275
DVU1949
115 combiner
DVU2423
DVU1419
115 combiner
DVU2423
DVU2588
115 combiner
DVU2547 115 tf
DVU2547
DVU0110
115 combiner
DVU0744 201 tf
DVU0813 201 tf
DVU1340
DVU2690
201 combiner
DVU1584
DVU0269
201 combiner
DVU2086 201 tf
DVU2106 201 tf
DVU2195 201 tf
DVU2275 201 tf
DVU2423
DVU0619
201 combiner
DVU2423
DVU0744
201 combiner
DVU3381 201 tf
DVUA0151
DVU1340
201 combiner

Warning: DVU2894 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
221 7.40e+02 cac..cAtACgacaAGgAgaa
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RegPredict
222 1.10e+03 cCGCCgtCagcCCcgtcctgaG
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RegPredict
385 1.90e+03 agGcCacGAcGcCCatctTTG
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RegPredict
386 1.00e+04 ttTCAGGaGat
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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 DVU2894

DVU2894 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains cog/ cog
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
Module neighborhood information for DVU2894

DVU2894 has total of 42 gene neighbors in modules 115, 201
Gene neighbors (42)
Gene Common Name Description Module membership
DVU0046 fliN flagellar motor switch protein FliN 115, 184
DVU0069 hypothetical protein DVU0069 193, 201
DVU0256 DEAD-box ATP dependent DNA helicase 194, 201
DVU0290 lipoprotein 115, 236
DVU0396 hup-1 DNA-binding protein HU 194, 201
DVU0573 creA creA protein 115, 269
DVU0655 phosphotransferase domain-containing protein 201, 211
DVU0741 hypothetical protein DVU0741 115, 198
DVU0744 sigma-54 dependent transcriptional regulator/response regulator 115, 198
DVU0803 sensor histidine kinase 198, 201
DVU0881 fusA elongation factor G 60, 115
DVU0963 7-cyano-7-deazaguanine reductase 194, 201
DVU0984 miaB (dimethylallyl)adenosine tRNA methylthiotransferase 115, 123
DVU1012 hemolysin-type calcium-binding repeat-containing protein 115, 194
DVU1030 universal stress protein 105, 201
DVU1359 hypothetical protein DVU1359 105, 115
DVU1410 hypothetical protein DVU1410 27, 201
DVU1422 OmpA family protein 60, 115
DVU1437 hypothetical protein DVU1437 201, 211
DVU1438 cobyrinic acid a,c-diamide synthase family protein 115, 201
DVU1472 ATP-dependent protease 115, 192
DVU1541 hypothetical protein DVU1541 60, 115
DVU1980 hypothetical protein DVU1980 115, 236
DVU2005 hypothetical protein DVU2005 175, 201
DVU2141 nucleic acid-binding protein 105, 115
DVU2313 pgl 6-phosphogluconolactonase 115, 236
DVU2360 FAD/NAD-binding family oxidoreductase 115, 192
DVU2446 panB 3-methyl-2-oxobutanoate hydroxymethyltransferase 62, 115
DVU2547 transcriptional regulator 194, 201
DVU2549 hypothetical protein DVU2549 193, 201
DVU2550 hypothetical protein DVU2550 193, 201
DVU2556 hypothetical protein DVU2556 105, 115
DVU2630 lipoprotein 115, 194
DVU2894 sigma-54 dependent transcriptional regulator 115, 201
DVU2895 hypothetical protein DVU2895 115, 192
DVU3153 hypothetical protein DVU3153 112, 115
DVU3213 hypothetical protein DVU3213 175, 201
DVU3220 sigma-54 dependent transcriptional regulator/response regulator 115, 198
DVU3221 sensor histidine kinase 115, 145
DVU3337 kdpC K+-transporting ATPase subunit C 13, 201
DVUA0031 hypothetical protein DVUA0031 115, 197
DVUA0097 radical SAM domain-containing protein 201, 211
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 DVU2894
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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