Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0277

AraC family transcriptional regulator

CircVis
Functional Annotations (7)
Function System
DNA gyrase inhibitor 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 DVU0277
(Mouseover regulator name to see its description)

DVU0277 is regulated by 19 influences and regulates 23 modules.
Regulators for DVU0277 (19)
Regulator Module Operator
DVU0525 55 tf
DVU0653 55 tf
DVU1584
DVU3023
55 combiner
DVU2086
DVU0539
55 combiner
DVU2086
DVU2567
55 combiner
DVU2086
DVU2588
55 combiner
DVU2086
DVU3142
55 combiner
DVU2275
DVU0110
55 combiner
DVU3023 55 tf
DVU3167
DVU1760
55 combiner
DVU3167
DVU2799
55 combiner
DVU3186
DVU2275
55 combiner
DVU0230 50 tf
DVU2567 50 tf
DVU3167 50 tf
DVU3167
DVU0629
50 combiner
DVU3167
DVU0936
50 combiner
DVU3186
DVU0653
50 combiner
DVU3193 50 tf

Warning: DVU0277 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
97 3.90e-03 ta.tgtc.T.aca.cCg.CcC
Loader icon
RegPredict
98 2.80e-02 AcgGcaAACGGggcGagGaGgagG
Loader icon
RegPredict
107 1.00e+02 CcgtA.ctctctaa.gcCG
Loader icon
RegPredict
108 9.50e+03 GtGGatGCCgtgcCg
Loader icon
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 DVU0277

DVU0277 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
DNA gyrase inhibitor 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 DVU0277

DVU0277 has total of 26 gene neighbors in modules 50, 55
Gene neighbors (26)
Gene Common Name Description Module membership
DVU0034 DSBA-like thioredoxin domain-containing protein 50, 63
DVU0226 hypothetical protein DVU0226 50, 255
DVU0277 AraC family transcriptional regulator 50, 55
DVU0347 hexapaptide repeat-containing transferase 55, 162
DVU0397 rare lipoprotein A 52, 55
DVU0734 uroporphyrinogen III synthase/methyltransferase 55, 282
DVU0736 purN phosphoribosylglycinamide formyltransferase 55, 181
DVU0752 amino acid ABC transporter amino acid-binding protein 50, 292
DVU0872 glycosyl transferase group 2 family protein 5, 55
DVU0951 molybdopterin biosynthesis MoeA protein 50, 195
DVU1086 hypothetical protein DVU1086 55, 179
DVU1087 hypothetical protein DVU1087 55, 56
DVU2223 hypothetical protein DVU2223 50, 78
DVU2238 RNA methyltransferase 55, 318
DVU2353 glycosyl transferase group 2 family protein 50, 229
DVU2613 hypothetical protein DVU2613 55, 275
DVU2734 None 55, 107
DVU2891 nikR nickel responsive regulator 55, 154
DVU2943 pyrE orotate phosphoribosyltransferase 52, 55
DVU2944 ErfK/YbiS/YcfS/YnhG family protein 55, 145
DVU3061 sensory box histidine kinase 55, 308
DVU3141 lipoprotein 50, 224
DVU3201 hypothetical protein DVU3201 27, 55
DVU3274 hypothetical protein DVU3274 55, 188
DVU3351 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase 50, 236
DVU3353 coaBC phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase 50, 346
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 DVU0277
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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