Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0954

organic solvent tolerance protein

CircVis
Functional Annotations (4)
Function System
Organic solvent tolerance protein OstA cog/ cog
response to organic substance go/ biological_process
cellular membrane organization go/ biological_process
outer membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0954
(Mouseover regulator name to see its description)

DVU0954 is regulated by 24 influences and regulates 0 modules.
Regulators for DVU0954 (24)
Regulator Module Operator
DVU0309
DVU0525
318 combiner
DVU0525 318 tf
DVU0813
DVU0230
318 combiner
DVU0916 318 tf
DVU0946 318 tf
DVU1518
DVU1730
318 combiner
DVU1584
DVU0653
318 combiner
DVU1645
DVUA0151
318 combiner
DVU3255
DVU0653
318 combiner
DVUA0151 318 tf
DVU0813
DVU0230
98 combiner
DVU0936 98 tf
DVU1584
DVU2114
98 combiner
DVU2036
DVU2114
98 combiner
DVU2036
DVU2251
98 combiner
DVU2036
DVU2532
98 combiner
DVU2114 98 tf
DVU2251 98 tf
DVU2423 98 tf
DVU2644
DVU0916
98 combiner
DVU2836 98 tf
DVU3142
DVU0813
98 combiner
DVU3186
DVU3080
98 combiner
DVUA0151 98 tf

Warning: DVU0954 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
189 2.10e+02 GAAAAA
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RegPredict
190 1.90e+04 actgccaAcgAtgccAggcC
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RegPredict
605 3.40e+02 CTtTTccg
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RegPredict
606 1.00e+04 GCaTTCCGaCgTcG
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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 DVU0954

DVU0954 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Organic solvent tolerance protein OstA cog/ cog
response to organic substance go/ biological_process
cellular membrane organization go/ biological_process
outer membrane go/ cellular_component
Module neighborhood information for DVU0954

DVU0954 has total of 40 gene neighbors in modules 98, 318
Gene neighbors (40)
Gene Common Name Description Module membership
DVU0112 deoxyribodipyrimidine photolyase 198, 318
DVU0280 glycosyl transferase group 1 family protein 98, 300
DVU0281 exopolysaccharide biosynthesis protein 98, 343
DVU0669 hypothetical protein DVU0669 98, 187
DVU0721 sensory box histidine kinase 198, 318
DVU0817 hypothetical protein DVU0817 98, 171
DVU0875 fumarylacetoacetate hydrolase family protein 318, 331
DVU0941 M16 family peptidase 16, 318
DVU0954 organic solvent tolerance protein 98, 318
DVU1428 pgm phosphoglucomutase 268, 318
DVU1446 heptosyltransferase family protein 318, 341
DVU1447 CgeB family protein 198, 318
DVU1448 hypothetical protein DVU1448 198, 318
DVU1449 anti-anti-sigma factor 71, 318
DVU1450 anti-sigma factor 71, 318
DVU1451 response regulator 318, 341
DVU1452 dtd D-tyrosyl-tRNA(Tyr) deacylase 14, 318
DVU1453 fadD long-chain-fatty-acid--CoA ligase 230, 318
DVU1681 mreB-2 rod shape-determining protein MreB 318, 348
DVU1683 hypothetical protein DVU1683 181, 318
DVU1684 gcvT glycine cleavage system T protein 318, 348
DVU1685 16S ribosomal RNA methyltransferase RsmE 318, 348
DVU1686 recombination factor protein RarA 318, 348
DVU1687 glycosyl transferase group 2 family protein 12, 318
DVU1688 1-acyl-sn-glycerol-3-phosphate acyltransferase 98, 187
DVU1690 TetR family transcriptional regulator 98, 263
DVU1793 hypothetical protein DVU1793 98, 297
DVU1796 hypothetical protein DVU1796 98, 343
DVU1798 hypothetical protein DVU1798 75, 98
DVU1809 nadB L-aspartate oxidase 75, 98
DVU1844 septum formation initiator family protein 318, 337
DVU1931 iron-sulfur cluster-binding protein 18, 98
DVU2083 relA GTP pyrophosphokinase 145, 318
DVU2238 RNA methyltransferase 55, 318
DVU2332 proC pyrroline-5-carboxylate reductase 64, 318
DVU2373 OMP85 family outer membrane protein 98, 135
DVU2569 peptidyl-prolyl cis-trans isomerase, FKBP-type 98, 187
DVU2576 oligopeptide ABC transporter ATP-binding protein 174, 318
DVU2674 succinate dehydrogenase and fumarate reductase iron-sulfur protein 172, 318
DVUA0074 sulfotransferase family protein 98, 288
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 DVU0954
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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