Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2097

transcriptional regulator

CircVis
Functional Annotations (4)
Function System
cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2097
(Mouseover regulator name to see its description)

DVU2097 is regulated by 22 influences and regulates 14 modules.
Regulators for DVU2097 (22)
Regulator Module Operator
DVU0436
DVU0230
257 combiner
DVU0619
DVU0230
257 combiner
DVU0653 257 tf
DVU1690 257 tf
DVU2251 257 tf
DVU2532
DVU3095
257 combiner
DVU2582
DVU0230
257 combiner
DVU2690 257 tf
DVU3080 257 tf
DVU3084 257 tf
DVU3381 257 tf
DVUA0024 257 tf
DVUA0057 257 tf
DVUA0151 257 tf
DVU0682
DVU2275
186 combiner
DVU1402 186 tf
DVU1561 186 tf
DVU2275
DVU2251
186 combiner
DVU2547 186 tf
DVU2547
DVU2832
186 combiner
DVU3167
DVU2582
186 combiner
DVUA0024 186 tf

Warning: DVU2097 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
355 1.40e+03 AGTTCAagTcT
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RegPredict
356 6.00e+03 TTTCTTTTTaT
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RegPredict
489 4.20e+02 tGaCaGtaGGCacggCaaaaG
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RegPredict
490 2.80e+03 .CagGtggCGcAgcTtC.tC
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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 DVU2097

DVU2097 is enriched for 4 functions in 3 categories.
Module neighborhood information for DVU2097

DVU2097 has total of 35 gene neighbors in modules 186, 257
Gene neighbors (35)
Gene Common Name Description Module membership
DVU0474 ISDvu4, transposase 257, 337
DVU0873 tsf elongation factor Ts 151, 186
DVU0874 rpsB 30S ribosomal protein S2 151, 186
DVU0958 rplI 50S ribosomal protein L9 186, 188
DVU0959 dnaB replicative DNA helicase 186, 188
DVU1021 hypothetical protein DVU1021 186, 188
DVU1022 SUF system FeS assembly ATPase SufC 186, 188
DVU1842 lipoprotein 186, 251
DVU1896 rpsT 30S ribosomal protein S20 186, 297
DVU1930 hypothetical protein 23, 186
DVU2028 hypothetical protein DVU2028 186, 273
DVU2097 transcriptional regulator 186, 257
DVU2143 fba fructose-1,6-bisphosphate aldolase, class II 186, 236
DVU2519 rpsI 30S ribosomal protein S9 151, 186
DVU2531 rpe ribulose-phosphate 3-epimerase 186, 292
DVU2533 pheT phenylalanyl-tRNA synthetase subunit beta 186, 306
DVU2534 pheS phenylalanyl-tRNA synthetase subunit alpha 186, 292
DVU2535 rplT 50S ribosomal protein L20 186, 258
DVU2536 rpmI 50S ribosomal protein L35 64, 186
DVU2537 infC translation initiation factor IF-3 186, 292
DVU2921 rpmG 50S ribosomal protein L33 186, 188
DVU3071 oxidoreductase 186, 188
DVU3103 tolB protein 186, 221
DVU3273 hypothetical protein DVU3273 145, 186
DVUA0008 nitrogenase molybdenum-iron cofactor biosynthesis protein NifN 257, 293
DVUA0014 glnB-3 nitrogen regulatory protein P-II 38, 257
DVUA0037 sugar transferase domain-containing protein 257, 335
DVUA0039 chain length determinant family protein 257, 328
DVUA0041 hypothetical protein DVUA0041 257, 335
DVUA0045 aminotransferase 200, 257
DVUA0056 hypothetical protein DVUA0056 47, 257
DVUA0062 hypothetical protein DVUA0062 200, 257
DVUA0063 Orn/DAP/Arg family decarboxylase 200, 257
DVUA0065 sensor histidine kinase 257, 328
DVUA0090 hypothetical protein DVUA0090 257, 335
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 DVU2097
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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