Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0895

RecD/TraA family helicase

CircVis
Functional Annotations (7)
Function System
ATP-dependent exoDNAse (exonuclease V), alpha subunit - helicase superfamily I member cog/ cog
nucleotide binding go/ molecular_function
exodeoxyribonuclease V activity go/ molecular_function
exodeoxyribonuclease V complex go/ cellular_component
nucleoside-triphosphatase activity go/ molecular_function
Homologous recombination kegg/ kegg pathway
recD_rel tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0895
(Mouseover regulator name to see its description)

DVU0895 is regulated by 25 influences and regulates 0 modules.
Regulators for DVU0895 (25)
Regulator Module Operator
DVU0946
DVU1690
78 combiner
DVU1547
DVU3142
78 combiner
DVU1690 78 tf
DVU2086
DVU0539
78 combiner
DVU2423
DVU2588
78 combiner
DVU3142
DVU0813
78 combiner
DVU3186
DVU1584
78 combiner
DVU3186
DVU2275
78 combiner
DVU3255
DVU2644
78 combiner
DVU3255
DVU2799
78 combiner
DVU0653 75 tf
DVU1063 75 tf
DVU1419 75 tf
DVU1584
DVU0653
75 combiner
DVU2036 75 tf
DVU2036
DVU1584
75 combiner
DVU2036
DVU2097
75 combiner
DVU2036
DVU2275
75 combiner
DVU2195 75 tf
DVU2423
DVU2588
75 combiner
DVU2423
DVU3142
75 combiner
DVU2547
DVU2588
75 combiner
DVU2588
DVU1142
75 combiner
DVU3381 75 tf
DVUA0151
DVU1547
75 combiner

Warning: DVU0895 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
147 5.50e+00 cTgTtgCATC.gacGccCc.tGgc
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RegPredict
148 4.40e+01 tTtTtctaga.Gtc
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RegPredict
153 6.20e+01 tAGca.caaAgg.ggcGg.tgtAA
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RegPredict
154 1.10e+02 tCaaGacaAaCGgtGcaaGgc
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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 DVU0895

DVU0895 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
ATP-dependent exoDNAse (exonuclease V), alpha subunit - helicase superfamily I member cog/ cog
nucleotide binding go/ molecular_function
exodeoxyribonuclease V activity go/ molecular_function
exodeoxyribonuclease V complex go/ cellular_component
nucleoside-triphosphatase activity go/ molecular_function
Homologous recombination kegg/ kegg pathway
recD_rel tigr/ tigrfam
Module neighborhood information for DVU0895

DVU0895 has total of 49 gene neighbors in modules 75, 78
Gene neighbors (49)
Gene Common Name Description Module membership
DVU0014 infA translation initiation factor IF-1 78, 344
DVU0054 dihydrouridine synthase family protein 56, 78
DVU0105 glutamine ABC transporter ATP-binding protein 78, 255
DVU0158 hypothetical protein DVU0158 17, 78
DVU0196 hypothetical protein DVU0196 78, 121
DVU0415 pepA cytosol aminopeptidase 54, 78
DVU0450 ribF riboflavin biosynthesis protein RibF 75, 278
DVU0451 chloride channel family protein 75, 327
DVU0746 ABC transporter permease 75, 126
DVU0784 hypothetical protein DVU0784 75, 344
DVU0785 rodA rod shape-determining protein RodA 75, 294
DVU0787 hypothetical protein DVU0787 75, 336
DVU0793 hypothetical protein DVU0793 78, 164
DVU0895 RecD/TraA family helicase 75, 78
DVU0896 NLP/P60 family lipoprotein 78, 146
DVU1008 hypothetical protein DVU1008 78, 344
DVU1026 uraA uracil permease 75, 344
DVU1033 competence/damage-inducible protein CinA protein, truncation 18, 78
DVU1041 tatC Sec-independent protein translocase TatC 78, 164
DVU1074 rpmH 50S ribosomal protein L34 18, 78
DVU1092 sodium-dependent symporter family protein 75, 344
DVU1245 ABC transporter ATP-binding protein 78, 347
DVU1346 xseA exodeoxyribonuclease VII large subunit 75, 195
DVU1349 geranylgeranyl diphosphate synthase 75, 195
DVU1355 hypothetical protein DVU1355 75, 128
DVU1357 hypothetical protein DVU1357 75, 87
DVU1533 miaA tRNA delta(2)-isopentenylpyrophosphate transferase 78, 187
DVU1797 ksgA dimethyladenosine transferase 75, 150
DVU1798 hypothetical protein DVU1798 75, 98
DVU1806 mgtE magnesium transporter 44, 75
DVU1808 nadA quinolinate synthetase 75, 258
DVU1809 nadB L-aspartate oxidase 75, 98
DVU1893 ATP-dependent protease 29, 78
DVU1928 lspA lipoprotein signal peptidase 52, 75
DVU1935 phosphonate ABC transporter permease 75, 336
DVU1936 phosphonate ABC transporter ATP-binding protein 75, 306
DVU2206 hypothetical protein DVU2206 78, 215
DVU2222 ssb single-strand binding protein 18, 78
DVU2223 hypothetical protein DVU2223 50, 78
DVU2225 acetyl-CoA carboxylase, carboxyl transferase, alpha/subunit beta 64, 78
DVU2229 motA-2 chemotaxis protein MotA 78, 170
DVU2230 deoD purine nucleoside phosphorylase 17, 78
DVU2254 thyX FAD-dependent thymidylate synthase 75, 228
DVU2255 ruvB Holliday junction DNA helicase RuvB 75, 228
DVU2339 ribosomal protein L11 methyltransferase 29, 75
DVU2341 amino acid ABC transporter permease 78, 347
DVU2931 sensory box histidine kinase 75, 262
DVU3056 hypothetical protein DVU3056 78, 251
DVU3165 hypothetical protein DVU3165 75, 336
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 DVU0895
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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