Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3023

sigma-54 dependent DNA-binding response regulator

CircVis
Functional Annotations (8)
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
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 DVU3023
(Mouseover regulator name to see its description)

DVU3023 is regulated by 20 influences and regulates 32 modules.
Regulators for DVU3023 (20)
Regulator Module Operator
DVU1063 214 tf
DVU1744 214 tf
DVU2785
DVU1517
214 combiner
DVU2785
DVU2195
214 combiner
DVU2953
DVU2960
214 combiner
DVU3023 214 tf
DVUA0024 214 tf
DVUA0057 214 tf
DVU0110
DVU0569
23 combiner
DVU0230 23 tf
DVU0309
DVU0653
23 combiner
DVU0653 23 tf
DVU1561 23 tf
DVU1754
DVU1561
23 combiner
DVU3167 23 tf
DVU3167
DVU0309
23 combiner
DVU3167
DVU0569
23 combiner
DVU3167
DVU3305
23 combiner
DVU3167
DVUA0100
23 combiner
DVUA0024 23 tf

Warning: DVU3023 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
45 1.70e+01 atGTGCtGCGgGG
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RegPredict
46 6.50e+00 CacatGaCaCagCCG
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RegPredict
407 1.80e+02 Aac.caC.ACa.gAtAgGaA
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RegPredict
408 1.80e+01 CGCA.gAGGCATGAC
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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 DVU3023

DVU3023 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
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
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
Module neighborhood information for DVU3023

DVU3023 has total of 53 gene neighbors in modules 23, 214
Gene neighbors (53)
Gene Common Name Description Module membership
DVU0084 aIF-2BI family translation initiation factor 9, 23
DVU0229 hypothetical protein DVU0229 214, 296
DVU0297 hypothetical protein DVU0297 214, 334
DVU0348 hypothetical protein DVU0348 23, 250
DVU0372 hypothetical protein DVU0372 53, 214
DVU0405 cobB-1 cobyrinic acid a,c-diamide synthase 126, 214
DVU0487 purE phosphoribosylaminoimidazole carboxylase, catalytic subunit 23, 176
DVU0546 hypothetical protein DVU0546 126, 214
DVU0620 L-PSP family endoribonuclease 63, 214
DVU0646 cobI precorrin-2 C20-methyltransferase 23, 176
DVU0647 iron compound ABC transporter periplasmic iron compount-binding protein 23, 211
DVU0648 iron compound ABC transporter ATP-binding protein 23, 176
DVU0649 iron compound ABC transporter permease 23, 176
DVU0650 chelatase 23, 176
DVU0652 cheV-2 chemotaxis protein CheV 83, 214
DVU0666 HD domain-containing protein 214, 309
DVU0843 hypothetical protein DVU0843 23, 137
DVU0940 GGDEF domain-containing protein 214, 303
DVU0988 carbohydrate kinase 23, 65
DVU0990 endonuclease III 23, 65
DVU0991 hypothetical protein DVU0991 23, 65
DVU1039 lipoprotein 23, 180
DVU1040 hisB imidazoleglycerol-phosphate dehydratase 23, 180
DVU1739 hypothetical protein DVU1739 121, 214
DVU1825 amidohydrolase family protein 27, 214
DVU1860 lnt apolipoprotein N-acyltransferase 9, 214
DVU1927 ileS isoleucyl-tRNA synthetase 23, 180
DVU1929 hypothetical protein DVU1929 23, 237
DVU1930 hypothetical protein 23, 186
DVU1989 hypothetical protein DVU1989 214, 309
DVU2257 hypothetical protein DVU2257 9, 214
DVU2322 UTP--glucose-1-phosphate uridylyltransferase 23, 174
DVU2391 hypothetical protein DVU2391 198, 214
DVU2463 recN DNA repair protein RecN 23, 141
DVU2464 hypothetical protein DVU2464 23, 30
DVU2478 pstC phosphate ABC transporter permease PstC 126, 214
DVU2584 CorA family protein 126, 214
DVU2666 phosphate ABC transporter permease 99, 214
DVU2761 hypothetical protein DVU2761 181, 214
DVU2825 pyruvate formate-lyase 1 activating enzyme 214, 222
DVU2843 DNA mismatch endonuclease Vsr 214, 334
DVU2844 hypothetical protein DVU2844 214, 334
DVU3023 sigma-54 dependent DNA-binding response regulator 23, 214
DVU3145 hydrogenase, b-type cytochrome subunit 214, 309
DVU3147 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 192, 214
DVU3154 deoxyribonucleotide triphosphate pyrophosphatase 23, 250
DVU3161 ABC transporter ATP-binding protein 23, 300
DVU3168 hemL glutamate-1-semialdehyde aminotransferase 23, 327
DVU3195 lipoprotein 161, 214
DVU3196 twin-arginine translocation pathway signal sequence domain-containing protein 87, 214
DVU3198 DNA polymerase III subunits gamma/tau 23, 180
DVU3199 hypothetical protein DVU3199 23, 220
DVU3200 recR recombination protein RecR 23, 220
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 DVU3023
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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