Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2532

MerR family transcriptional regulator

CircVis
Functional Annotations (4)
Function System
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2532
(Mouseover regulator name to see its description)

DVU2532 is regulated by 23 influences and regulates 26 modules.
Regulators for DVU2532 (23)
Regulator Module Operator
DVU0916 332 tf
DVU0916
DVU1745
332 combiner
DVU1628
DVU0916
332 combiner
DVU1645
DVU0916
332 combiner
DVU1690 332 tf
DVU2686 332 tf
DVU2686
DVU1584
332 combiner
DVU2827 332 tf
DVU2836
DVU1628
332 combiner
DVU3080 332 tf
DVU3255
DVU3186
332 combiner
DVU0854
DVU2251
232 combiner
DVU1144 232 tf
DVU1690 232 tf
DVU1730 232 tf
DVU2251 232 tf
DVU2557 232 tf
DVU2686 232 tf
DVU2686
DVU3193
232 combiner
DVU2686
DVU3220
232 combiner
DVU2832 232 tf
DVU3193
DVU2251
232 combiner
DVUA0024 232 tf

Warning: DVU2532 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
443 4.00e-02 tAacAcggggaaacAGGAGaatc
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RegPredict
444 3.50e+00 CGatAt.GGTTtTcA
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RegPredict
631 7.40e+00 tctTttc.TTT
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RegPredict
632 1.30e+03 GggtGccgTTG
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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 DVU2532

DVU2532 is enriched for 4 functions in 2 categories.
Enrichment Table (4)
Function System
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for DVU2532

DVU2532 has total of 43 gene neighbors in modules 232, 332
Gene neighbors (43)
Gene Common Name Description Module membership
DVU0302 chemotaxis protein CheX 232, 332
DVU0674 His/Glu/Gln/Arg/opine ABC transporter permease 309, 332
DVU0690 hypothetical protein DVU0690 272, 332
DVU0789 mreB-1 rod shape-determining protein MreB 282, 332
DVU0837 rimM 16S rRNA processing protein RimM 18, 232
DVU0838 hypothetical protein DVU0838 18, 232
DVU0925 rfbA glucose-1-phosphate thymidylyltransferase 331, 332
DVU0936 hypothetical protein DVU0936 146, 232
DVU0939 hypothetical protein DVU0939 8, 332
DVU0942 Fur family transcriptional regulator 122, 232
DVU0986 hypothetical protein DVU0986 132, 232
DVU0987 heavy metal-binding domain-containing protein 132, 232
DVU1093 HAD family hydrolase 132, 232
DVU1190 sensory box protein 232, 343
DVU1367 tatA twin arginine translocase protein A 121, 232
DVU1372 hypothetical protein DVU1372 232, 249
DVU1373 divIVA cell-division initiation protein DivIVA 232, 249
DVU1374 hypothetical protein DVU1374 232, 249
DVU1375 hypothetical protein DVU1375 232, 249
DVU1377 ilvH acetolactate synthase 3 regulatory subunit 232, 249
DVU1378 ilvC ketol-acid reductoisomerase 232, 249
DVU1392 NLP/P60 family protein 146, 232
DVU1409 hypothetical protein DVU1409 56, 332
DVU1572 CarD family transcriptional regulator 16, 332
DVU1612 ACT domain-containing protein 16, 232
DVU1631 hypothetical protein DVU1631 330, 332
DVU1633 PTS system transporter subunit IIB 330, 332
DVU1634 hypothetical protein DVU1634 330, 332
DVU1679 idi isopentenyl-diphosphate delta-isomerase 279, 332
DVU1801 hypothetical protein DVU1801 279, 332
DVU1832 hypothetical protein DVU1832 332, 339
DVU1834 pyruvate carboxylase 143, 232
DVU1837 competence protein 331, 332
DVU1845 hypothetical protein DVU1845 332, 337
DVU1894 hypothetical protein DVU1894 132, 332
DVU2308 hypothetical protein DVU2308 215, 332
DVU2354 glycosyl transferase group 2 family protein 283, 332
DVU2532 MerR family transcriptional regulator 232, 332
DVU2965 hypothetical protein DVU2965 232, 285
DVU3117 hypothetical protein DVU3117 308, 332
DVU3187 hup-4 DNA-binding protein HU 146, 232
DVU3226 hypothetical protein DVU3226 71, 332
DVU3228 cheY-3 chemotaxis protein CheY 157, 332
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 DVU2532
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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