Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2675

LuxR family transcriptional regulator

CircVis
Functional Annotations (9)
Function System
Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain 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
intracellular go/ cellular_component
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2675
(Mouseover regulator name to see its description)

DVU2675 is regulated by 16 influences and regulates 38 modules.
Regulators for DVU2675 (16)
Regulator Module Operator
DVU0110 229 tf
DVU0110
DVU1144
229 combiner
DVU1331
DVU0110
229 combiner
DVU1517 229 tf
DVU1572
DVU2547
229 combiner
DVU3313
DVU0110
229 combiner
DVU0679 279 tf
DVU0916 279 tf
DVU1144 279 tf
DVU1561
DVU0916
279 combiner
DVU1572
DVU1759
279 combiner
DVU1628 279 tf
DVU1645
DVU1964
279 combiner
DVU1674 279 tf
DVU1759 279 tf
DVU2827 279 tf

Warning: DVU2675 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
437 3.40e+01 GTaTgttcGTGGTAtgaTGa
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RegPredict
438 2.90e+02 ccATaTcCgTTgaCttgcgTg
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RegPredict
533 1.40e+00 tgcTGa.gtAtTTtttgc.TGAca
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RegPredict
534 1.50e+02 AaGGaActGGTcAT
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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 DVU2675

DVU2675 is enriched for 9 functions in 3 categories.
Module neighborhood information for DVU2675

DVU2675 has total of 60 gene neighbors in modules 229, 279
Gene neighbors (60)
Gene Common Name Description Module membership
DVU0035 hypothetical protein DVU0035 157, 279
DVU0163 lipoprotein 170, 279
DVU0322 eno phosphopyruvate hydratase 229, 236
DVU0407 rare lipoprotein A family protein 16, 229
DVU0564 ISDvu4, transposase, truncation 279, 283
DVU0627 ptB phosphotransbutyrylase 192, 229
DVU0682 DNA-binding protein 141, 229
DVU0790 radical SAM family protein 134, 229
DVU0999 thio:disulfide interchange protein 107, 279
DVU1016 hypothetical protein DVU1016 225, 279
DVU1145 hypothetical protein DVU1145 279, 283
DVU1181 response regulator 141, 279
DVU1331 LysR family transcriptional regulator 179, 279
DVU1333 hypothetical protein DVU1333 179, 279
DVU1405 hypothetical protein DVU1405 229, 308
DVU1678 rimI ribosomal-protein-alanine acetyltransferase 219, 279
DVU1679 idi isopentenyl-diphosphate delta-isomerase 279, 332
DVU1689 hypothetical protein DVU1689 127, 279
DVU1701 hypothetical protein DVU1701 239, 279
DVU1760 TetR family transcriptional regulator 170, 279
DVU1780 hypothetical protein DVU1780 169, 229
DVU1781 hypothetical protein DVU1781 169, 229
DVU1782 iron-sulfur cluster-binding protein 169, 229
DVU1783 hypothetical protein DVU1783 169, 229
DVU1784 short chain dehydrogenase/reductase family oxidoreductase 169, 229
DVU1785 MarC membrane protein 169, 229
DVU1801 hypothetical protein DVU1801 279, 332
DVU1862 GGDEF domain-containing protein 94, 229
DVU1901 peptidyl-prolyl cis-trans isomerase domain-containing protein 12, 229
DVU1905 hypothetical protein DVU1905 170, 279
DVU1916 hypothetical protein DVU1916 229, 245
DVU1921 hynB-1 periplasmic 229, 348
DVU1922 hynA-1 periplasmic 229, 348
DVU1923 hupD hydrogenase expression/formation protein HupD 229, 308
DVU1924 hypC hydrogenase assembly chaperone HypC/HupF 109, 229
DVU1925 GDSL family lipase 109, 229
DVU2004 ISDvu4, transposase 279, 283
DVU2013 hydroxylamine reductase 27, 229
DVU2014 metallo-beta-lactamase family protein 53, 229
DVU2021 hypothetical protein DVU2021 229, 273
DVU2264 hypothetical protein DVU2264 11, 279
DVU2353 glycosyl transferase group 2 family protein 50, 229
DVU2416 hypothetical protein DVU2416 229, 268
DVU2460 hypothetical protein DVU2460 229, 236
DVU2648 hypothetical protein DVU2648 219, 279
DVU2649 hypothetical protein DVU2649 245, 279
DVU2654 hypothetical protein DVU2654 279, 313
DVU2657 6-pyruvoyl tetrahydrobiopterin synthase 215, 279
DVU2669 hypothetical protein DVU2669 179, 279
DVU2675 LuxR family transcriptional regulator 229, 279
DVU2727 hypothetical protein DVU2727 20, 279
DVU2770 response regulator 71, 229
DVU2937 TPR domain/response regulator receiver domain-containing protein 71, 229
DVU2956 sigma-54 dependent transcriptional regulator 279, 285
DVU2969 acetoacetyl-CoA synthase 225, 279
DVU3035 methyl-accepting chemotaxis protein 137, 229
DVU3049 hemerythrin family protein 35, 229
DVU3083 hypothetical protein DVU3083 157, 279
DVU3313 LysR family transcriptional regulator 5, 279
DVU3327 SMR family multidrug efflux pump 94, 279
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 DVU2675
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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