Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2644

GntR family transcriptional regulator

CircVis
Functional Annotations (6)
Function System
Transcriptional regulators cog/ cog
fatty-acyl-CoA 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 fatty acid metabolic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2644
(Mouseover regulator name to see its description)

DVU2644 is regulated by 19 influences and regulates 40 modules.
Regulators for DVU2644 (19)
Regulator Module Operator
DVU0230 63 tf
DVU0749
DVU0539
63 combiner
DVU0749
DVU3334
63 combiner
DVU0749
DVUA0024
63 combiner
DVU2036
DVU1144
63 combiner
DVU2114 63 tf
DVU2527
DVU0653
63 combiner
DVU2836
DVU0569
63 combiner
DVU2836
DVU1788
63 combiner
DVU2836
DVU3193
63 combiner
DVU1572
DVU2547
230 combiner
DVU2275 230 tf
DVU2423 230 tf
DVU2527
DVU3305
230 combiner
DVU2547
DVU2319
230 combiner
DVU2547
DVU3229
230 combiner
DVU2644 230 tf
DVU2675 230 tf
DVU2802
DVU2275
230 combiner

Warning: DVU2644 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
123 1.20e+00 aaGacaCcAcAgGAtAGGAa
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RegPredict
124 3.90e+02 gGAGgCATGAC
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RegPredict
439 9.60e-04 aaaatCAAtAacAcatccTTTtCA
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RegPredict
440 1.30e-01 TACcgGtgACGGCA..tGgCA
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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 DVU2644

DVU2644 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Transcriptional regulators cog/ cog
fatty-acyl-CoA 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 fatty acid metabolic process go/ biological_process
Module neighborhood information for DVU2644

DVU2644 has total of 51 gene neighbors in modules 63, 230
Gene neighbors (51)
Gene Common Name Description Module membership
DVU0034 DSBA-like thioredoxin domain-containing protein 50, 63
DVU0056 cheV-1 chemotaxis protein CheV 63, 343
DVU0113 hisI phosphoribosyl-AMP cyclohydrolase 113, 230
DVU0227 hypothetical protein DVU0227 63, 255
DVU0334 D-alanine--D-alanine ligase 63, 195
DVU0335 3-deoxy-D-manno-octulosonic-acid transferase 206, 230
DVU0395 HIT family protein 63, 194
DVU0454 hypothetical protein DVU0454 63, 157
DVU0477 icd isocitrate dehydrogenase, NADP-dependent 230, 262
DVU0575 hypothetical protein DVU0575 63, 226
DVU0619 sigma-54 dependent transcriptional regulator 63, 198
DVU0620 L-PSP family endoribonuclease 63, 214
DVU0656 hypothetical protein DVU0656 63, 303
DVU0671 hypothetical protein DVU0671 228, 230
DVU0672 hypothetical protein DVU0672 99, 230
DVU0704 lepB signal peptidase I 230, 258
DVU0745 ABC transporter periplasmic substrate-binding protein 215, 230
DVU0854 NirD protein 63, 226
DVU0953 tyrS tyrosyl-tRNA synthetase 139, 230
DVU1054 HAD superfamily hydrolase 65, 230
DVU1090 recA recombinase A 63, 323
DVU1186 mazG nucleoside triphosphate pyrophosphohydrolase 166, 230
DVU1223 hypothetical protein DVU1223 228, 230
DVU1408 hypothetical protein DVU1408 63, 196
DVU1434 hypothetical protein DVU1434 57, 63
DVU1453 fadD long-chain-fatty-acid--CoA ligase 230, 318
DVU1469 rpsA 30S ribosomal protein S1 76, 230
DVU1537 lipoprotein 63, 297
DVU1579 cysS cysteinyl-tRNA synthetase 63, 282
DVU1616 hypothetical protein DVU1616 63, 323
DVU1677 tpiA triosephosphate isomerase 17, 230
DVU1820 yajC preprotein translocase, YajC subunit 63, 297
DVU1877 polysaccharide deacetylase family protein 63, 215
DVU1888 ATP-NAD kinase domain-containing protein 63, 128
DVU2263 outer membrane autotransporter 121, 230
DVU2433 hypothetical protein DVU2433 230, 291
DVU2434 hypothetical protein DVU2434 230, 254
DVU2471 oxidoreductase, selenocysteine-containing 63, 223
DVU2521 aroK shikimate kinase 228, 230
DVU2586 ABC transporter ATP-binding protein 230, 323
DVU2612 hypothetical protein DVU2612 63, 249
DVU2639 hypothetical protein DVU2639 57, 63
DVU2644 GntR family transcriptional regulator 63, 230
DVU2946 hypothetical protein DVU2946 137, 230
DVU3118 hypothetical protein DVU3118 230, 254
DVU3119 AMP-binding protein 81, 230
DVU3253 phenylacetate-coenzyme A ligase 230, 306
DVU3281 hypothetical protein DVU3281 52, 63
DVU3299 hypothetical protein DVU3299 76, 230
DVU3345 None 63, 120
DVU3359 hypothetical protein DVU3359 57, 63
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 DVU2644
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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