Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2378

AraC family transcriptional regulator

CircVis
Functional Annotations (7)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2378
(Mouseover regulator name to see its description)

DVU2378 is regulated by 24 influences and regulates 6 modules.
Regulators for DVU2378 (24)
Regulator Module Operator
DVU0653 191 tf
DVU0679 191 tf
DVU0744
DVU0942
191 combiner
DVU0813
DVU0942
191 combiner
DVU0942 191 tf
DVU1340
DVU1744
191 combiner
DVU2675
DVU1340
191 combiner
DVU3080 191 tf
DVU3095 191 tf
DVU0653 34 tf
DVU0679 34 tf
DVU0679
DVU0942
34 combiner
DVU0744
DVU0942
34 combiner
DVU0813
DVU0942
34 combiner
DVU0942 34 tf
DVU1340
DVU1744
34 combiner
DVU1744 34 tf
DVU2086
DVU1340
34 combiner
DVU2675 34 tf
DVU2675
DVU1340
34 combiner
DVU3080 34 tf
DVU3095 34 tf
DVU3167 34 tf
DVU3229
DVU0942
34 combiner

Warning: DVU2378 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
67 0.00e+00 AcaTTGAaAATCaTaaTCAATA
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RegPredict
68 1.50e-01 ACACcaAtAtaCCGcaACaTG
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RegPredict
365 0.00e+00 AcaTTGAaAATCaTaaTCAATA
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RegPredict
366 3.10e-01 ACACcaAtAtaCCGcaACaTG
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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 DVU2378

DVU2378 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for DVU2378

DVU2378 has total of 27 gene neighbors in modules 34, 191
Gene neighbors (27)
Gene Common Name Description Module membership
DVU0273 hypothetical protein DVU0273 34, 191
DVU0303 hypothetical protein DVU0303 34, 191
DVU0304 hypothetical protein DVU0304 34, 191
DVU0762 hypothetical protein DVU0762 34, 191
DVU0763 GGDEF domain-containing protein 34, 191
DVU2377 hypothetical protein DVU2377 34, 191
DVU2378 AraC family transcriptional regulator 34, 191
DVU2379 M16 family peptidase 155, 191
DVU2380 ABC transporter ATP-binding protein 155, 191
DVU2381 hypothetical protein DVU2381 27, 34
DVU2383 TonB dependent receptor domain-containing protein 34, 191
DVU2388 tolQ-1 tolQ protein 155, 191
DVU2389 biopolymer ExbD/TolR family transporter 155, 191
DVU2390 TonB domain-containing protein 155, 191
DVU2564 bioF 8-amino-7-oxononanoate synthase 34, 254
DVU2571 feoB ferrous iron transport protein B 34, 191
DVU2572 ferrous iron transport protein A 34, 191
DVU2573 hypothetical protein DVU2573 34, 191
DVU2574 ferrous ion transport protein 34, 191
DVU2680 flavodoxin 34, 191
DVU2681 hypothetical protein DVU2681 34, 191
DVU3122 hypothetical protein DVU3122 191, 330
DVU3124 hypothetical protein DVU3124 34, 269
DVU3330 hypothetical protein DVU3330 17, 34
DVU3331 hypothetical protein DVU3331 34, 191
DVU3332 heavy metal translocating P-type ATPase 34, 191
DVU3333 hypothetical protein DVU3333 34, 191
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 DVU2378
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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