Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3080

transcriptional regulator

CircVis
Functional Annotations (4)
Function System
Predicted transcriptional regulator cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
zinc ion binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU3080
(Mouseover regulator name to see its description)

DVU3080 is regulated by 27 influences and regulates 38 modules.
Regulators for DVU3080 (27)
Regulator Module Operator
DVU0309 187 tf
DVU0539 187 tf
DVU2633 187 tf
DVU2644
DVU0916
187 combiner
DVU2644
DVU2633
187 combiner
DVU2686
DVU3255
187 combiner
DVU2827 187 tf
DVU2836 187 tf
DVU3142
DVU0813
187 combiner
DVU3255 187 tf
DVUA0143 187 tf
DVUA0151 187 tf
DVU0269 8 tf
DVU0309 8 tf
DVU0539 8 tf
DVU1331
DVU2114
8 combiner
DVU1572 8 tf
DVU1572
DVU1760
8 combiner
DVU1645
DVU2114
8 combiner
DVU2106
DVU2633
8 combiner
DVU2114 8 tf
DVU2114
DVU1760
8 combiner
DVU2532 8 tf
DVU2686 8 tf
DVU2686
DVU3255
8 combiner
DVU2827 8 tf
DVU2836
DVU3313
8 combiner

Warning: DVU3080 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
15 0.00e+00 AAAatttcacaaTcttcttacAaT
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RegPredict
16 0.00e+00 atATcAaaataAaa.TtcAAaca
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RegPredict
357 1.10e+02 GCA.Ggtgg.gaAacgagtTga
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RegPredict
358 1.10e+03 TTCCTTgCGAt
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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 DVU3080

DVU3080 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted transcriptional regulator cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
zinc ion binding go/ molecular_function
Module neighborhood information for DVU3080

DVU3080 has total of 38 gene neighbors in modules 8, 187
Gene neighbors (38)
Gene Common Name Description Module membership
DVU0252 hypothetical protein DVU0252 8, 246
DVU0268 hypothetical protein DVU0268 8, 343
DVU0472 hypothetical protein DVU0472 8, 246
DVU0473 hypothetical protein DVU0473 8, 246
DVU0553 hypothetical protein DVU0553 8, 246
DVU0630 hypothetical protein DVU0630 8, 246
DVU0669 hypothetical protein DVU0669 98, 187
DVU0916 redox-sensing transcriptional repressor Rex 8, 16
DVU0939 hypothetical protein DVU0939 8, 332
DVU1015 hypothetical protein DVU1015 8, 170
DVU1019 hypothetical protein DVU1019 48, 187
DVU1020 HD domain/sensory box protein 54, 187
DVU1155 hypothetical protein DVU1155 8, 170
DVU1285 response regulator 8, 143
DVU1351 MarC membrane protein 187, 288
DVU1361 lpxB lipid A disaccharide synthase 187, 268
DVU1480 hypothetical protein DVU1480 187, 233
DVU1533 miaA tRNA delta(2)-isopentenylpyrophosphate transferase 78, 187
DVU1637 hypothetical protein DVU1637 8, 170
DVU1638 hypothetical protein DVU1638 8, 170
DVU1639 hypothetical protein DVU1639 8, 170
DVU1646 arsC arsenate reductase 8, 246
DVU1688 1-acyl-sn-glycerol-3-phosphate acyltransferase 98, 187
DVU1859 hypothetical protein DVU1859 187, 219
DVU1966 hypothetical protein DVU1966 187, 219
DVU2114 sigma-54 dependent transcriptional regulator/response regulator 187, 246
DVU2128 hypothetical protein DVU2128 187, 283
DVU2145 chloramphenicol acetyltransferase 8, 170
DVU2146 hypothetical protein DVU2146 8, 170
DVU2392 CesT family type III secretion chaperone 187, 246
DVU2409 solute-binding family 3 protein 48, 187
DVU2569 peptidyl-prolyl cis-trans isomerase, FKBP-type 98, 187
DVU2725 hypothetical protein DVU2725 8, 246
DVU2726 None 8, 246
DVU3080 transcriptional regulator 8, 187
DVUA0017 hypothetical protein DVUA0017 159, 187
DVUA0067 hypothetical protein DVUA0067 121, 187
DVUA0068 hypothetical protein DVUA0068 163, 187
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 DVU3080
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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