Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2547

transcriptional regulator

CircVis
Functional Annotations (4)
Function System
cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2547
(Mouseover regulator name to see its description)

DVU2547 is regulated by 27 influences and regulates 64 modules.
Regulators for DVU2547 (27)
Regulator Module Operator
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
DVU0596 194 tf
DVU0619
DVU1063
194 combiner
DVU0744
DVU0230
194 combiner
DVU0813 194 tf
DVU0854 194 tf
DVU1340
DVU1730
194 combiner
DVU1547 194 tf
DVU1584 194 tf
DVU1628 194 tf
DVU2086 194 tf
DVU2275 194 tf
DVU2423 194 tf
DVU2423
DVU0744
194 combiner
DVU2894
DVU0525
194 combiner
DVU3381 194 tf

Warning: DVU2547 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
371 5.50e+03 ggcgCAtcctc
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RegPredict
372 1.10e+04 ATAgCCAG
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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 DVU2547

DVU2547 is enriched for 4 functions in 3 categories.
Module neighborhood information for DVU2547

DVU2547 has total of 36 gene neighbors in modules 194, 201
Gene neighbors (36)
Gene Common Name Description Module membership
DVU0069 hypothetical protein DVU0069 193, 201
DVU0256 DEAD-box ATP dependent DNA helicase 194, 201
DVU0395 HIT family protein 63, 194
DVU0396 hup-1 DNA-binding protein HU 194, 201
DVU0595 hypothetical protein DVU0595 4, 194
DVU0655 phosphotransferase domain-containing protein 201, 211
DVU0683 hflC protein 194, 198
DVU0684 hflK protein 167, 194
DVU0725 hypothetical protein DVU0725 4, 194
DVU0803 sensor histidine kinase 198, 201
DVU0853 hypothetical protein DVU0853 157, 194
DVU0910 fliM flagellar motor switch protein FliM 194, 198
DVU0963 7-cyano-7-deazaguanine reductase 194, 201
DVU1012 hemolysin-type calcium-binding repeat-containing protein 115, 194
DVU1030 universal stress protein 105, 201
DVU1410 hypothetical protein DVU1410 27, 201
DVU1437 hypothetical protein DVU1437 201, 211
DVU1438 cobyrinic acid a,c-diamide synthase family protein 115, 201
DVU1603 aat leucyl/phenylalanyl-tRNA--protein transferase 123, 194
DVU1830 hypothetical protein DVU1830 194, 198
DVU2005 hypothetical protein DVU2005 175, 201
DVU2324 copper-translocating P-type ATPase 4, 194
DVU2468 lpxK tetraacyldisaccharide 4'-kinase 4, 194
DVU2470 membrane protein 158, 194
DVU2489 hypothetical protein DVU2489 167, 194
DVU2547 transcriptional regulator 194, 201
DVU2548 acpD ACP phosphodiesterase 110, 194
DVU2549 hypothetical protein DVU2549 193, 201
DVU2550 hypothetical protein DVU2550 193, 201
DVU2630 lipoprotein 115, 194
DVU2894 sigma-54 dependent transcriptional regulator 115, 201
DVU2974 hypothetical protein DVU2974 4, 194
DVU3213 hypothetical protein DVU3213 175, 201
DVU3337 kdpC K+-transporting ATPase subunit C 13, 201
DVU3344 hypothetical protein DVU3344 167, 194
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 DVU2547
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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