Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0945

sensor histidine kinase

CircVis
Functional Annotations (6)
Function System
Signal transduction histidine kinase, nitrogen specific cog/ cog
two-component sensor activity go/ molecular_function
ATP binding go/ molecular_function
signal transduction go/ biological_process
membrane go/ cellular_component
peptidyl-histidine phosphorylation go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0945
(Mouseover regulator name to see its description)

DVU0945 is regulated by 28 influences and regulates 0 modules.
Regulators for DVU0945 (28)
Regulator Module Operator
DVU0539 343 tf
DVU0916
DVU2835
343 combiner
DVU0946 343 tf
DVU1745 343 tf
DVU2036
DVU0629
343 combiner
DVU2036
DVU0916
343 combiner
DVU2036
DVU2114
343 combiner
DVU2114 343 tf
DVU2251 343 tf
DVU2557 343 tf
DVU2788 343 tf
DVU2835 343 tf
DVU2836 343 tf
DVU2836
DVU3193
343 combiner
DVU2909 343 tf
DVU3186 343 tf
DVU3255
DVU3186
343 combiner
DVUA0143 343 tf
DVU0946
DVU2114
88 combiner
DVU1156 88 tf
DVU1572
DVU2114
88 combiner
DVU1572
DVU3255
88 combiner
DVU2114 88 tf
DVU2836 88 tf
DVU3023 88 tf
DVU3142 88 tf
DVU3186 88 tf
DVU3255 88 tf

Warning: DVU0945 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
173 9.80e+02 TTcTTTAATTAAA
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RegPredict
174 2.60e+03 gAAcAGCc
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RegPredict
651 1.30e-03 T.a.AtActcgAtaaagttGt
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RegPredict
652 1.20e+00 cAgtagtaTaCgcAaaataTcAa
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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 DVU0945

DVU0945 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Signal transduction histidine kinase, nitrogen specific cog/ cog
two-component sensor activity go/ molecular_function
ATP binding go/ molecular_function
signal transduction go/ biological_process
membrane go/ cellular_component
peptidyl-histidine phosphorylation go/ biological_process
Module neighborhood information for DVU0945

DVU0945 has total of 32 gene neighbors in modules 88, 343
Gene neighbors (32)
Gene Common Name Description Module membership
DVU0056 cheV-1 chemotaxis protein CheV 63, 343
DVU0074 polysaccharide biosynthesis domain-containing protein 164, 343
DVU0106 glnP glutamine ABC transporter permease 88, 300
DVU0222 hypothetical protein DVU0222 272, 343
DVU0259 DNA-binding response regulator 343, 346
DVU0267 hypothetical protein DVU0267 343, 346
DVU0268 hypothetical protein DVU0268 8, 343
DVU0281 exopolysaccharide biosynthesis protein 98, 343
DVU0321 pantothenate kinase 88, 164
DVU0945 sensor histidine kinase 88, 343
DVU1027 hypothetical protein DVU1027 88, 154
DVU1190 sensory box protein 232, 343
DVU1406 purM phosphoribosylaminoimidazole synthetase 88, 146
DVU1470 ppiC peptidyl-prolyl cis-trans isomerase C 132, 343
DVU1652 HIT family protein 88, 128
DVU1762 hypothetical protein DVU1762 33, 343
DVU1778 cation efflux family protein 88, 171
DVU1796 hypothetical protein DVU1796 98, 343
DVU1831 None 88, 300
DVU2227 hypothetical protein DVU2227 164, 343
DVU2372 hypothetical protein DVU2372 88, 163
DVU2443 hypothetical protein DVU2443 272, 343
DVU2607 hypothetical protein DVU2607 88, 308
DVU2608 motA-3 flagellar motor protein MotA 88, 303
DVU2650 hypothetical protein DVU2650 16, 88
DVU2847 hypothetical protein DVU2847 272, 343
DVU3039 hypothetical protein DVU3039 33, 343
DVU3085 hypothetical protein DVU3085 88, 303
DVU3088 DEAD-box ATP dependent DNA helicase 88, 163
DVU3149 sppA signal peptide peptidase SppA, 36K type 56, 88
DVU3182 dcrA methyl-accepting chemotaxis protein DcrA 53, 343
DVU3375 cell division ATP-binding protein FtsE 48, 343
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 DVU0945
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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