Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2240

hydantoinase/oxoprolinase family protein

CircVis
Functional Annotations (2)
Function System
N-methylhydantoinase A/acetone carboxylase, beta subunit cog/ cog
hydrolase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2240
(Mouseover regulator name to see its description)

DVU2240 is regulated by 24 influences and regulates 0 modules.
Regulators for DVU2240 (24)
Regulator Module Operator
DVU0110 277 tf
DVU0653 277 tf
DVU0749 277 tf
DVU0749
DVU0653
277 combiner
DVU0946 277 tf
DVU0946
DVU1730
277 combiner
DVU1518
DVU3066
277 combiner
DVU1547
DVU0110
277 combiner
DVU2567 277 tf
DVU2788
DVU0110
277 combiner
DVU2788
DVU0946
277 combiner
DVU2953 277 tf
DVU3066 277 tf
DVU0118 296 tf
DVU0269 296 tf
DVU1142 296 tf
DVU1561 296 tf
DVU1788 296 tf
DVU2195
DVU2251
296 combiner
DVU2557
DVU1745
296 combiner
DVU2557
DVU2547
296 combiner
DVU2644
DVU2909
296 combiner
DVU2960 296 tf
DVU3313
DVU2909
296 combiner

Warning: DVU2240 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
529 3.30e-03 A.attActtGCAgAa.GtGaAtAt
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RegPredict
530 1.60e+01 aGAcaGaCTGTACA
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RegPredict
567 1.90e+02 CTctTgAAaAaaaTA
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RegPredict
568 1.50e+03 TCgTGCcTtcatCATGCtgt
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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 DVU2240

DVU2240 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
N-methylhydantoinase A/acetone carboxylase, beta subunit cog/ cog
hydrolase activity go/ molecular_function
Module neighborhood information for DVU2240

DVU2240 has total of 56 gene neighbors in modules 277, 296
Gene neighbors (56)
Gene Common Name Description Module membership
DVU0005 lipoprotein 83, 296
DVU0082 hypothetical protein DVU0082 83, 277
DVU0229 hypothetical protein DVU0229 214, 296
DVU0261 universal stress protein 296, 346
DVU0262 hypothetical protein DVU0262 296, 346
DVU0265 hypothetical protein DVU0265 296, 346
DVU0266 hypothetical protein DVU0266 296, 346
DVU0270 sensory box histidine kinase 277, 346
DVU0271 response regulator 83, 277
DVU0352 aminotransferase 141, 277
DVU0485 hypothetical protein DVU0485 161, 277
DVU0640 pomA chemotaxis protein PomA 105, 296
DVU0659 hypothetical protein DVU0659 27, 277
DVU0686 iron-sulfur cluster-binding protein 83, 277
DVU0688 hypothetical protein DVU0688 185, 277
DVU0697 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase 172, 296
DVU0720 HAMP domain-containing protein 272, 296
DVU0748 acs acetyl-CoA synthetase 150, 296
DVU0766 transporter 26, 296
DVU0805 hypothetical protein DVU0805 53, 296
DVU0806 chemotaxis protein CheY 53, 296
DVU0815 AsmA family protein 35, 277
DVU0907 hypothetical protein DVU0907 162, 277
DVU0908 iron-sulfur cluster-binding protein 54, 277
DVU0934 hypothetical protein DVU0934 296, 315
DVU0935 methyl-accepting chemotaxis protein 122, 296
DVU0961 hypothetical protein DVU0961 277, 296
DVU0969 amino acid transporter LysE 83, 277
DVU1000 M24 family peptidase 172, 296
DVU1007 cobU cobinamide kinase/cobinamide phosphate guanylyltransferase 83, 277
DVU1189 hypothetical protein DVU1189 9, 277
DVU1227 hypothetical protein DVU1227 267, 296
DVU1362 hypothetical protein DVU1362 30, 277
DVU1363 rfbD dTDP-4-dehydrorhamnose reductase 30, 277
DVU1364 rfbB dTDP-glucose 4,6-dehydratase 30, 277
DVU1366 lipoprotein 30, 277
DVU1413 hypothetical protein DVU1413 192, 296
DVU1595 cheR-1 chemotaxis protein methyltransferase 274, 277
DVU1800 None 269, 296
DVU1892 glycosyl transferase group 2 family protein 94, 277
DVU1909 acpS 4'-phosphopantetheinyl transferase 26, 296
DVU1993 cation transporter E1-E2 family ATPase 37, 296
DVU2239 glycosy hydrolase family protein 17, 277
DVU2240 hydantoinase/oxoprolinase family protein 277, 296
DVU2244 glgA glycogen synthase 83, 277
DVU2245 mutT/nudix family protein 269, 296
DVU2302 glutathione-regulated potassium-efflux system protein KefB 141, 277
DVU2357 HD domain-containing protein 83, 277
DVU2430 RNA-binding protein 249, 296
DVU2431 hypothetical protein DVU2431 175, 296
DVU2529 pgk phosphoglycerate kinase 262, 296
DVU2545 iron-containing alcohol dehydrogenase 35, 277
DVU2546 sensory box histidine kinase 35, 277
DVU2575 M20/M25/M40 family peptidase 180, 277
DVU2897 hypothetical protein DVU2897 62, 277
DVU3259 xth exodeoxyribonuclease III 153, 296
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 DVU2240
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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