Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0309

LysR family transcriptional regulator

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0309
(Mouseover regulator name to see its description)

DVU0309 is regulated by 18 influences and regulates 48 modules.
Regulators for DVU0309 (18)
Regulator Module Operator
DVU0804 22 tf
DVU1584
DVU1517
22 combiner
DVU2557
DVU2675
22 combiner
DVU2675
DVU3313
22 combiner
DVU2799 22 tf
DVU2802
DVU0569
22 combiner
DVU2802
DVU2989
22 combiner
DVU2909
DVU0110
22 combiner
DVU2909
DVU3193
22 combiner
DVU3255
DVU1561
22 combiner
DVU3313 22 tf
DVU1967 280 tf
DVU2557
DVU1156
280 combiner
DVU2577
DVU0596
280 combiner
DVU2675 280 tf
DVU2886 280 tf
DVU3305 280 tf
DVUA0151 280 tf

Warning: DVU0309 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
43 1.40e-04 Gcatgct.ctTGCat
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RegPredict
44 8.70e+00 aAggGcGgGGaTGaCG.CTCTCc
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RegPredict
535 2.30e+01 tCCaaCTgtttttcaGAtAGa
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RegPredict
536 1.10e+02 cGaCATCAatgcCAa
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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 DVU0309

DVU0309 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for DVU0309

DVU0309 has total of 48 gene neighbors in modules 22, 280
Gene neighbors (48)
Gene Common Name Description Module membership
DVU0043 fliQ flagellar biosynthetic protein FliQ 22, 286
DVU0172 iron-sulfur cluster-binding protein 280, 311
DVU0173 thiosulfate reductase 280, 311
DVU0186 hypothetical protein DVU0186 280, 311
DVU0250 hypothetical protein DVU0250 62, 280
DVU0251 hypothetical protein DVU0251 96, 280
DVU0307 flagella basal body rod domain-containing protein 22, 286
DVU0308 hypothetical protein DVU0308 181, 280
DVU0309 LysR family transcriptional regulator 22, 280
DVU0318 hypothetical protein 22, 286
DVU0320 hypothetical protein DVU0320 22, 286
DVU0325 hypD hydrogenase expression/formation protein HypD 22, 62
DVU0409 hypothetical protein DVU0409 22, 184
DVU0410 hypothetical protein DVU0410 22, 286
DVU0518 hypothetical protein DVU0518 22, 286
DVU0520 flagellar hook-associated protein FlgL 22, 184
DVU0862 bifunctional flagellar protein FliS/hypothetical protein 22, 184
DVU0863 flagellar hook-associated protein 2 22, 184
DVU1169 methyl-accepting chemotaxis protein 280, 311
DVU1441 flagellin 22, 286
DVU1443 flgE flagellar hook protein FlgE 22, 286
DVU1444 flgD basal-body rod modification protein FlgD 22, 286
DVU1805 GGDEF domain-containing protein 22, 286
DVU1963 hypothetical protein DVU1963 22, 286
DVU2065 hypothetical protein DVU2065 22, 286
DVU2110 L-lactate permease 280, 311
DVU2510 penicillin-binding protein 86, 280
DVU2560 hypothetical protein DVU2560 280, 311
DVU2562 acyl carrier protein 280, 311
DVU2563 beta-ketoacyl synthase 280, 311
DVU2802 GntR family transcriptional regulator 280, 311
DVU2803 hypothetical protein DVU2803 280, 311
DVU2804 metallo-beta-lactamase family protein 27, 280
DVU2805 P47K family cobalamin synthesis protein 280, 311
DVU2806 MotA/TolQ/ExbB proton channel family protein 280, 311
DVU2807 biopolymer ExbD/TolR family transporter 280, 311
DVU2991 hypothetical protein DVU2991 22, 286
DVU3001 hypothetical protein DVU3001 22, 184
DVU3002 hypothetical protein DVU3002 22, 286
DVU3004 radical SAM domain-containing protein 22, 125
DVU3005 aminotransferase 22, 145
DVU3006 polysaccharide biosynthesis protein/methyltransferase 22, 180
DVU3014 asparagine synthetase, glutamine-hydrolyzing 22, 211
DVU3232 flhA flagellar biosynthesis protein FlhA 22, 286
DVU3290 hypothetical protein DVU3290 280, 311
DVU3291 glutamate synthase, iron-sulfur cluster-binding subunit 280, 311
DVU3292 pyridine nucleotide-disulfide oxidoreductase 46, 280
DVU3312 hypothetical protein DVU3312 280, 311
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 DVU0309
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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