Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2628

hypothetical protein

CircVis
Functional Annotations (1)
Function System
binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2628
(Mouseover regulator name to see its description)

DVU2628 is regulated by 23 influences and regulates 0 modules.
Regulators for DVU2628 (23)
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
DVU0230 234 tf
DVU0525 234 tf
DVU1584
DVU2251
234 combiner
DVU2036
DVU2532
234 combiner
DVU2423 234 tf
DVU2527
DVU0653
234 combiner
DVU2644
DVU0653
234 combiner
DVU2644
DVU2582
234 combiner
DVU3080
DVU0653
234 combiner
DVUA0057 234 tf
DVUA0151 234 tf

Warning: DVU2628 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
447 4.80e-01 ATatTCtaTgTCcAAaagCatT
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RegPredict
448 3.10e+01 aGgtATatActaaAAtaGtat
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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 DVU2628

DVU2628 is enriched for 1 functions in 2 categories.
Enrichment Table (1)
Function System
binding go/ molecular_function
Module neighborhood information for DVU2628

DVU2628 has total of 39 gene neighbors in modules 234, 326
Gene neighbors (39)
Gene Common Name Description Module membership
DVU0070 Ser/Thr protein phosphatase family protein 7, 234
DVU0306 hypothetical protein DVU0306 320, 326
DVU0351 cytidine 5'monophosphate N-acetylneuraminic acid synthetase /polysaccharide biosynthesis protein 234, 341
DVU0488 purD phosphoribosylamine--glycine ligase 193, 326
DVU1034 hypothetical protein DVU1034 202, 326
DVU1035 glucokinase 234, 341
DVU1226 hypothetical protein DVU1226 224, 326
DVU1239 hypothetical protein DVU1239 234, 341
DVU1297 hypothetical protein DVU1297 202, 326
DVU1400 methyl-accepting chemotaxis protein 283, 326
DVU1508 hypothetical protein DVU1508 234, 341
DVU1610 nadE glutamine-dependent NAD+ synthetase 166, 326
DVU1846 pgsA CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase 123, 326
DVU1858 cold shock domain-containing protein 234, 341
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
DVU2283 hypothetical protein DVU2283 234, 341
DVU2336 carboxyl-terminal protease 234, 341
DVU2456 hypothetical protein DVU2456 134, 234
DVU2476 gltA oxidoreductase 137, 326
DVU2517 hypothetical protein DVU2517 203, 234
DVU2628 hypothetical protein 234, 326
DVU2656 hypothetical protein DVU2656 326, 329
DVU2753 hypothetical protein 97, 326
DVU2755 hypothetical protein DVU2755 27, 234
DVU2773 hypothetical protein DVU2773 242, 326
DVU2874 hypothetical protein DVU2874 234, 341
DVU2939 hypothetical protein DVU2939 97, 326
DVU3110 oxidoreductase 234, 341
DVU3211 hypothetical protein DVU3211 7, 234
DVU3325 hypothetical protein DVU3325 234, 341
DVUA0043 polysaccharide deacetylase family protein 234, 335
DVUA0055 hypothetical protein DVUA0055 200, 234
DVUA0096 major facilitator superfamily protein 234, 341
DVUA0139 outer membrane autotransporter 234, 340
DVUA0140 hypothetical protein DVUA0140 234, 340
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 DVU2628
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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