Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0542

universal stress protein

CircVis
Functional Annotations (2)
Function System
Universal stress protein UspA and related nucleotide-binding proteins cog/ cog
response to stress go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0542
(Mouseover regulator name to see its description)

DVU0542 is regulated by 17 influences and regulates 0 modules.
Regulators for DVU0542 (17)
Regulator Module Operator
DVU0230 205 tf
DVU0594
DVU0653
205 combiner
DVU0653 205 tf
DVU0653
DVU2633
205 combiner
DVU1561
DVU0539
205 combiner
DVU1561
DVU2832
205 combiner
DVU2036 205 tf
DVU2036
DVU2114
205 combiner
DVU3167 205 tf
DVU3167
DVU0569
205 combiner
DVU0653
DVU2582
70 combiner
DVU0653
DVU2633
70 combiner
DVU1517 70 tf
DVU1518
DVU1561
70 combiner
DVU1561
DVUA0024
70 combiner
DVU2086
DVU1517
70 combiner
DVU2832 70 tf

Warning: DVU0542 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
137 4.40e-02 tTTgat.G.cTctAcaaaaa
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RegPredict
138 6.40e-01 tTcT.GtGtt
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RegPredict
393 1.00e+03 aAAcaataatgtctAaaCaaaAaA
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RegPredict
394 2.10e+04 caTccCCCATc
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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 DVU0542

DVU0542 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Universal stress protein UspA and related nucleotide-binding proteins cog/ cog
response to stress go/ biological_process
Module neighborhood information for DVU0542

DVU0542 has total of 30 gene neighbors in modules 70, 205
Gene neighbors (30)
Gene Common Name Description Module membership
DVU0050 motA-1 chemotaxis protein MotA 123, 205
DVU0053 sulfate permease 109, 205
DVU0145 response regulator 37, 205
DVU0361 acetolactate synthase 1 regulatory subunit 99, 205
DVU0382 hypothetical protein DVU0382 2, 70
DVU0416 GGDEF domain-containing protein 66, 205
DVU0476 hypothetical protein DVU0476 70, 205
DVU0542 universal stress protein 70, 205
DVU0543 hypothetical protein DVU0543 70, 100
DVU0544 hypothetical protein DVU0544 70, 205
DVU0614 hypothetical protein DVU0614 205, 291
DVU0639 pomB chemotaxis protein PomB 37, 205
DVU0673 hypothetical protein DVU0673 70, 289
DVU0921 5-nitroimidazole antibiotic resistance protein 70, 244
DVU1085 phoU phosphate transport system protein PhoU 70, 239
DVU1379 hypothetical protein DVU1379 70, 90
DVU1384 pyrR bifunctional pyrimidine regulatory protein PyrR uracil phosphoribosyltransferase 123, 205
DVU1481 nuclease domain-containing protein 70, 239
DVU2151 hypothetical protein DVU2151 70, 259
DVU2152 hypothetical protein DVU2152 70, 76
DVU2199 hypothetical protein DVU2199 70, 92
DVU2213 nuclease domain-containing protein 70, 100
DVU2775 hypothetical protein DVU2775 109, 205
DVU2781 hypothetical protein DVU2781 102, 205
DVU3082 methyl-accepting chemotaxis protein 193, 205
DVU3129 hypothetical protein DVU3129 70, 130
DVU3140 capsular polysaccharide transport protein 123, 205
DVU3265 tartrate dehydratase subunit beta 77, 205
DVU3286 hypothetical protein DVU3286 61, 205
DVU3317 hypothetical protein DVU3317 25, 70
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 DVU0542
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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