Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2939

hypothetical protein DVU2939

CircVis
Functional Annotations (1)
Function System
ATP-utilizing enzymes of the PP-loop superfamily cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2939
(Mouseover regulator name to see its description)

DVU2939 is regulated by 25 influences and regulates 0 modules.
Regulators for DVU2939 (25)
Regulator Module Operator
DVU0230
DVU1083
326 combiner
DVU1063 326 tf
DVU1083
DVU2832
326 combiner
DVU1754
DVU1419
326 combiner
DVU1754
DVU3334
326 combiner
DVU2785 326 tf
DVU2785
DVU0230
326 combiner
DVU2785
DVU3142
326 combiner
DVU3255
DVU0594
326 combiner
DVU3255
DVU1744
326 combiner
DVU3334
DVU2832
326 combiner
DVUA0057
DVU3066
326 combiner
DVU0539 97 tf
DVU0653 97 tf
DVU0679
DVU2832
97 combiner
DVU0916 97 tf
DVU1063 97 tf
DVU1517 97 tf
DVU1517
DVU0539
97 combiner
DVU1754
DVU2785
97 combiner
DVU2886
DVU1754
97 combiner
DVU3186 97 tf
DVU3193
DVU2114
97 combiner
DVU3255
DVU3186
97 combiner
DVUA0151 97 tf

Warning: DVU2939 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
187 2.30e-02 AaCGAcgTgCaCcgc.CAaaAGA
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RegPredict
188 1.10e-01 GacAaagtgcAaCatc.ta..aac
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RegPredict
619 3.60e+03 aCCTCCAtga
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RegPredict
620 5.80e+03 ACCtggagcaCatcCtcat
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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 DVU2939

DVU2939 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
ATP-utilizing enzymes of the PP-loop superfamily cog/ cog
Module neighborhood information for DVU2939

DVU2939 has total of 39 gene neighbors in modules 97, 326
Gene neighbors (39)
Gene Common Name Description Module membership
DVU0078 hypothetical protein DVU0078 2, 97
DVU0139 sensor histidine kinase 31, 97
DVU0306 hypothetical protein DVU0306 320, 326
DVU0488 purD phosphoribosylamine--glycine ligase 193, 326
DVU0622 sensor histidine kinase/response regulator 97, 311
DVU1034 hypothetical protein DVU1034 202, 326
DVU1083 phoB phosphate regulon transcriptional regulator PhoB 13, 97
DVU1156 sigma-54 dependent transcriptional regulator /response regulator 97, 345
DVU1224 nfo endonuclease IV 25, 97
DVU1226 hypothetical protein DVU1226 224, 326
DVU1297 hypothetical protein DVU1297 202, 326
DVU1400 methyl-accepting chemotaxis protein 283, 326
DVU1610 nadE glutamine-dependent NAD+ synthetase 166, 326
DVU1726 hypothetical protein DVU1726 97, 265
DVU1846 pgsA CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase 123, 326
DVU1885 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B 202, 326
DVU1981 nucleotide-binding protein 84, 326
DVU2025 hypothetical protein DVU2025 273, 326
DVU2149 hypothetical protein DVU2149 32, 326
DVU2237 cobalamin biosynthesis protein CobD 84, 326
DVU2269 hypothetical protein DVU2269 76, 97
DVU2270 hypothetical protein DVU2270 97, 118
DVU2271 pyruvate formate-lyase activating enzyme 97, 329
DVU2272 formate acetyltransferase 25, 97
DVU2476 gltA oxidoreductase 137, 326
DVU2628 hypothetical protein 234, 326
DVU2656 hypothetical protein DVU2656 326, 329
DVU2665 phosphate ABC transporter permease 68, 97
DVU2736 hypothetical protein DVU2736 15, 97
DVU2750 cbiD cobalamin biosynthesis protein CbiD 68, 97
DVU2751 hypothetical protein DVU2751 97, 160
DVU2752 rhodanese-like domain-containing protein 97, 119
DVU2753 hypothetical protein 97, 326
DVU2773 hypothetical protein DVU2773 242, 326
DVU2939 hypothetical protein DVU2939 97, 326
DVU3170 cobJ precorrin-3b C17-methyltransferase 25, 97
DVUA0004 DNA-binding protein HU 68, 97
DVUA0066 patatin family phospholipase 38, 97
DVUA0093 chromate transport family protein 97, 197
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 DVU2939
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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