Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0118

sigma-54 dependent transcriptional regulator/response regulator

CircVis
Functional Annotations (9)
Function System
Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0118
(Mouseover regulator name to see its description)

DVU0118 is regulated by 16 influences and regulates 17 modules.
Regulators for DVU0118 (16)
Regulator Module Operator
DVU0539
DVU1745
112 combiner
DVU1645
DVU2275
112 combiner
DVU1645
DVU3255
112 combiner
DVU2195 112 tf
DVU2547
DVU0539
112 combiner
DVU2547
DVU3142
112 combiner
DVU3080
DVU2275
112 combiner
DVU0063 105 tf
DVU1561
DVU2588
105 combiner
DVU1584
DVU2275
105 combiner
DVU2036
DVU2275
105 combiner
DVU2195 105 tf
DVU2423
DVU1547
105 combiner
DVU2423
DVU2588
105 combiner
DVU2547
DVU0539
105 combiner
DVU3220 105 tf

Warning: DVU0118 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
203 4.80e+02 tcGtCGacatcCCCCTcCGgttCt
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RegPredict
204 1.30e+01 GCcgcaa.cgcCttc.tca
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RegPredict
215 3.00e+04 ACTTCaCgaC
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RegPredict
216 6.50e+03 GCCcGaAcgGttGacGcGTTCGcC
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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 DVU0118

DVU0118 is enriched for 9 functions in 3 categories.
Module neighborhood information for DVU0118

DVU0118 has total of 55 gene neighbors in modules 105, 112
Gene neighbors (55)
Gene Common Name Description Module membership
DVU0032 hypothetical protein DVU0032 112, 211
DVU0118 sigma-54 dependent transcriptional regulator/response regulator 105, 112
DVU0119 sensor histidine kinase 82, 112
DVU0120 ABC transporter substrate-binding protein 82, 112
DVU0254 hypothetical protein DVU0254 105, 167
DVU0289 moaC molybdenum cofactor biosynthesis protein C 105, 112
DVU0294 glycosyl transferase group 2 family protein 31, 105
DVU0482 sensory box histidine kinase/response regulator 105, 112
DVU0581 response regulator/anti-anti-sigma factor 105, 112
DVU0582 sensory box histidine kinase 105, 112
DVU0584 transposase 105, 304
DVU0608 methyl-accepting chemotaxis protein 105, 198
DVU0631 hypothetical protein DVU0631 109, 112
DVU0634 hypothetical protein DVU0634 105, 112
DVU0640 pomA chemotaxis protein PomA 105, 296
DVU0755 sensor histidine kinase 105, 198
DVU0814 bacterioferritin comigratory protein 112, 211
DVU0992 cheV-3 chemotaxis protein CheV 105, 198
DVU1030 universal stress protein 105, 201
DVU1136 host-nuclease inhibitor protein Gam 112, 231
DVU1219 hypothetical protein DVU1219 35, 112
DVU1338 hypothetical protein DVU1338 112, 198
DVU1359 hypothetical protein DVU1359 105, 115
DVU1404 radical SAM domain-containing protein 86, 105
DVU1419 sigma-54 dependent transcriptional regulator/response regulator 112, 123
DVU1535 hypothetical protein DVU1535 31, 105
DVU1547 sensory box protein 35, 112
DVU1549 hypothetical protein DVU1549 112, 198
DVU1853 hypothetical protein DVU1853 105, 175
DVU2138 hypothetical protein DVU2138 105, 178
DVU2141 nucleic acid-binding protein 105, 115
DVU2195 hypothetical protein DVU2195 105, 311
DVU2312 hypothetical protein DVU2312 105, 123
DVU2337 M24/M37 family peptidase 26, 112
DVU2352 glycosyl transferase group 2 family protein 76, 112
DVU2410 sodB superoxide dismutase, Fe 105, 321
DVU2429 hypothetical protein DVU2429 105, 109
DVU2472 hypothetical protein DVU2472 105, 112
DVU2556 hypothetical protein DVU2556 105, 115
DVU2588 DNA-binding response regulator 112, 281
DVU2668 glmU bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase 105, 106
DVU2707 virion morphogenesis protein 105, 239
DVU2708 virion morphogenesis protein 105, 239
DVU2732 hypothetical protein DVU2732 38, 112
DVU2739 pyruvate phosphate dikinase PEP/pyruvate binding subunit 112, 304
DVU2896 hypothetical protein 30, 112
DVU2994 glycosyl transferase group 2 family protein 15, 112
DVU3010 aminotransferase 112, 304
DVU3012 hypothetical protein DVU3012 95, 112
DVU3062 sensor histidine kinase/response regulator 105, 321
DVU3153 hypothetical protein DVU3153 112, 115
DVU3209 hypothetical protein DVU3209 112, 211
DVU3268 hypothetical protein DVU3268 105, 175
DVU3336 potassium channel histidine kinase domain-containing protein/universal stress protein 13, 112
DVU3388 lipoprotein 105, 112
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 DVU0118
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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