Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3186

hypothetical protein DVU3186

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

Cytoscape Web
Regulation information for DVU3186
(Mouseover regulator name to see its description)

DVU3186 is regulated by 22 influences and regulates 61 modules.
Regulators for DVU3186 (22)
Regulator Module Operator
DVU0525 164 tf
DVU0539 164 tf
DVU0606 164 tf
DVU0606
DVU0916
164 combiner
DVU0946
DVU1144
164 combiner
DVU0946
DVU1690
164 combiner
DVU2799 164 tf
DVU2836 164 tf
DVU3193 164 tf
DVU3193
DVU0916
164 combiner
DVU3255 164 tf
DVU3255
DVU0936
164 combiner
DVUA0151 164 tf
DVU0946
DVU0916
56 combiner
DVU1547 56 tf
DVU1572
DVU1760
56 combiner
DVU1584
DVU2114
56 combiner
DVU1690 56 tf
DVU2799 56 tf
DVU2836 56 tf
DVU2836
DVU3313
56 combiner
DVUA0151
DVU1547
56 combiner

Warning: DVU3186 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
109 0.00e+00 GTCTT.GAAg.cAA.GTaAGC
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RegPredict
110 6.20e-05 TGTg.tcGTaTGgg.TTtcTGCT
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RegPredict
313 2.30e+03 aaAaacctaGcaaAA
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RegPredict
314 4.00e+03 CccgtcttGccgaCGtccggc
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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 DVU3186

DVU3186 is enriched for 1 functions in 2 categories.
Enrichment Table (1)
Function System
nucleotide binding go/ molecular_function
Module neighborhood information for DVU3186

DVU3186 has total of 32 gene neighbors in modules 56, 164
Gene neighbors (32)
Gene Common Name Description Module membership
DVU0054 dihydrouridine synthase family protein 56, 78
DVU0074 polysaccharide biosynthesis domain-containing protein 164, 343
DVU0153 hypothetical protein DVU0153 56, 164
DVU0157 thiL thiamin-monophosphate kinase 56, 164
DVU0321 pantothenate kinase 88, 164
DVU0502 hypothetical protein DVU0502 29, 56
DVU0657 HSP20 family protein 164, 303
DVU0792 hypothetical protein DVU0792 56, 164
DVU0793 hypothetical protein DVU0793 78, 164
DVU0879 hypothetical protein DVU0879 56, 283
DVU0880 hypothetical protein DVU0880 56, 143
DVU0886 thioesterase family protein 56, 171
DVU1041 tatC Sec-independent protein translocase TatC 78, 164
DVU1087 hypothetical protein DVU1087 55, 56
DVU1242 vacJ lipoprotein 48, 164
DVU1407 radical SAM domain-containing protein 56, 164
DVU1409 hypothetical protein DVU1409 56, 332
DVU1576 ispE 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase 29, 56
DVU1663 permease 56, 282
DVU1664 engB ribosome biogenesis GTP-binding protein YsxC 56, 143
DVU1665 aroQ 3-dehydroquinate dehydratase 56, 143
DVU1666 efp elongation factor P 29, 56
DVU1954 nadD nicotinate (nicotinamide) nucleotide adenylyltransferase 56, 146
DVU2227 hypothetical protein DVU2227 164, 343
DVU2300 hypothetical protein DVU2300 56, 143
DVU2323 hypothetical protein DVU2323 164, 303
DVU2340 His/Glu/Gln/Arg/opine ABC transporter permease 56, 143
DVU3054 radical SAM domain-containing protein 56, 143
DVU3149 sppA signal peptide peptidase SppA, 36K type 56, 88
DVU3150 rpsA 30S ribosomal protein S1 56, 143
DVU3174 ubiE ubiquinone/menaquinone biosynthesis methlytransferase UbiE 164, 327
DVU3186 hypothetical protein DVU3186 56, 164
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 DVU3186
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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