Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0026

hypothetical protein DVU0026

CircVis
Functional Annotations (2)
Function System
Dienelactone hydrolase and related enzymes cog/ cog
hydrolase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0026
(Mouseover regulator name to see its description)

DVU0026 is regulated by 19 influences and regulates 0 modules.
Regulators for DVU0026 (19)
Regulator Module Operator
DVU0653
DVU1690
247 combiner
DVU0744
DVU2690
247 combiner
DVU1402
DVU1730
247 combiner
DVU1572
DVU0936
247 combiner
DVU1730 247 tf
DVU2423
DVU0619
247 combiner
DVU3381
DVU1730
247 combiner
DVU0230 261 tf
DVU0379
DVU0525
261 combiner
DVU0629 261 tf
DVU0653
DVU2251
261 combiner
DVU0936 261 tf
DVU1754 261 tf
DVU1754
DVU0379
261 combiner
DVU1788
DVU0230
261 combiner
DVU2394
DVU2251
261 combiner
DVU2557
DVU0936
261 combiner
DVU2686
DVU2960
261 combiner
DVUA0024 261 tf

Warning: DVU0026 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
471 6.60e-03 at.ttAcAtT.ttaTaTgaa
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RegPredict
472 3.50e+02 ta.Aaaaa.aCAaAt
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RegPredict
497 1.40e+03 GcTgTtCa
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RegPredict
498 1.20e+04 ACAGCAGACCCATGCGGAGGACAC
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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 DVU0026

DVU0026 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Dienelactone hydrolase and related enzymes cog/ cog
hydrolase activity go/ molecular_function
Module neighborhood information for DVU0026

DVU0026 has total of 54 gene neighbors in modules 247, 261
Gene neighbors (54)
Gene Common Name Description Module membership
DVU0026 hypothetical protein DVU0026 247, 261
DVU0049 OmpA family protein 222, 247
DVU0094 methyl-accepting chemotaxis protein 247, 289
DVU0100 TonB-dependent receptor 247, 256
DVU0101 UbiE/COQ5 family methlytransferase 69, 247
DVU0103 cation ABC transporter ATP-binding protein 247, 334
DVU0130 phosphoglycolate phosphatase 185, 247
DVU0164 cation efflux family protein 109, 261
DVU0233 hypothetical protein DVU0233 247, 281
DVU0272 hypothetical protein DVU0272 51, 261
DVU0329 hypothetical protein DVU0329 106, 261
DVU0360 ilvB-1 acetolactate synthase catalytic subunit 99, 247
DVU0436 TetR family transcriptional regulator 68, 261
DVU0446 sodium/solute symporter family protein 247, 334
DVU0533 hmc operon protein 4 189, 247
DVU0534 hmc operon protein 3 189, 247
DVU0588 formate dehydrogenase subunit beta 189, 247
DVU0593 L-lysine exporter 53, 247
DVU0678 hypothetical protein DVU0678 53, 247
DVU0791 methylated DNA-protein cysteine methyltransferase DNA binding subunit 247, 267
DVU1071 hypothetical protein DVU1071 65, 261
DVU1667 FtsK/SpoIIIE family protein 51, 261
DVU1763 hypothetical protein DVU1763 25, 261
DVU1764 hypothetical protein DVU1764 113, 261
DVU1765 thiH thiamine biosynthesis protein ThiH 95, 261
DVU1766 aspartate ammonia-lyase 124, 261
DVU1767 biotin synthase 95, 261
DVU1768 GTP-binding protein 95, 261
DVU1802 hypothetical protein DVU1802 26, 261
DVU1856 hypothetical protein DVU1856 144, 261
DVU1956 heptosyltransferase family protein 137, 261
DVU2090 EF hand domain-containing protein 46, 247
DVU2268 hypothetical protein DVU2268 31, 261
DVU2277 hypothetical protein DVU2277 261, 341
DVU2301 lipoprotein 92, 261
DVU2311 None 37, 261
DVU2350 gid tRNA (uracil-5-)-methyltransferase Gid 25, 261
DVU2466 flocculin repeat-containing protein 51, 261
DVU2570 GGDEF domain/HAMP domain-containing protein 69, 247
DVU2687 hypothetical protein DVU2687 247, 269
DVU2730 tail fiber protein 181, 247
DVU2760 hypothetical protein DVU2760 25, 261
DVU2772 hypothetical protein DVU2772 160, 261
DVU2829 hypothetical protein DVU2829 38, 247
DVU2849 tail fiber protein 247, 314
DVU2909 MarR family transcriptional regulator 57, 261
DVU2999 methionyl-tRNA formyltransferase 247, 271
DVU3202 TatD family hydrolase 57, 261
DVU3244 hypothetical protein DVU3244 247, 289
DVU3366 def polypeptide deformylase 227, 261
DVU3372 hypothetical protein DVU3372 247, 311
DVU3384 zraP zinc resistance-associated protein 53, 247
DVUA0036 TPR domain-containing protein 53, 247
DVUA0089 hypothetical protein DVUA0089 90, 247
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 DVU0026
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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