Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1690

TetR family transcriptional regulator

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1690
(Mouseover regulator name to see its description)

DVU1690 is regulated by 22 influences and regulates 40 modules.
Regulators for DVU1690 (22)
Regulator Module Operator
DVU0813
DVU0230
98 combiner
DVU0936 98 tf
DVU1584
DVU2114
98 combiner
DVU2036
DVU2114
98 combiner
DVU2036
DVU2251
98 combiner
DVU2036
DVU2532
98 combiner
DVU2114 98 tf
DVU2251 98 tf
DVU2423 98 tf
DVU2644
DVU0916
98 combiner
DVU2836 98 tf
DVU3142
DVU0813
98 combiner
DVU3186
DVU3080
98 combiner
DVUA0151 98 tf
DVU0030
DVU3080
263 combiner
DVU0309 263 tf
DVU0629 263 tf
DVU1745 263 tf
DVU2114 263 tf
DVU2527 263 tf
DVU2686 263 tf
DVU3186 263 tf

Warning: DVU1690 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
189 2.10e+02 GAAAAA
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RegPredict
190 1.90e+04 actgccaAcgAtgccAggcC
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RegPredict
501 0.00e+00 aacg.TtTATggtaT
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RegPredict
502 3.60e-02 ataa.attGAAA.At
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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 DVU1690

DVU1690 is enriched for 5 functions in 3 categories.
Module neighborhood information for DVU1690

DVU1690 has total of 37 gene neighbors in modules 98, 263
Gene neighbors (37)
Gene Common Name Description Module membership
DVU0030 GntR family transcriptional regulator 263, 311
DVU0280 glycosyl transferase group 1 family protein 98, 300
DVU0281 exopolysaccharide biosynthesis protein 98, 343
DVU0369 hypothetical protein DVU0369 170, 263
DVU0560 hypothetical protein DVU0560 190, 263
DVU0618 hypothetical protein DVU0618 233, 263
DVU0669 hypothetical protein DVU0669 98, 187
DVU0817 hypothetical protein DVU0817 98, 171
DVU0954 organic solvent tolerance protein 98, 318
DVU1257 RNA-binding protein 18, 263
DVU1561 molybdenum-binding protein 242, 263
DVU1564 hypothetical protein DVU1564 263, 274
DVU1688 1-acyl-sn-glycerol-3-phosphate acyltransferase 98, 187
DVU1690 TetR family transcriptional regulator 98, 263
DVU1705 type I restriction-modification enzyme, S subunit 233, 263
DVU1793 hypothetical protein DVU1793 98, 297
DVU1796 hypothetical protein DVU1796 98, 343
DVU1798 hypothetical protein DVU1798 75, 98
DVU1809 nadB L-aspartate oxidase 75, 98
DVU1931 iron-sulfur cluster-binding protein 18, 98
DVU2000 hypothetical protein DVU2000 111, 263
DVU2007 nuclease 111, 263
DVU2096 hypothetical protein DVU2096 245, 263
DVU2106 sigma-54 dependent transcriptional regulator 111, 263
DVU2182 hypothetical protein DVU2182 170, 263
DVU2183 hypothetical protein DVU2183 170, 263
DVU2198 hypothetical protein DVU2198 244, 263
DVU2373 OMP85 family outer membrane protein 98, 135
DVU2451 L-lactate permease family protein 157, 263
DVU2452 hypothetical protein DVU2452 263, 331
DVU2569 peptidyl-prolyl cis-trans isomerase, FKBP-type 98, 187
DVU2651 hypothetical protein DVU2651 219, 263
DVU2718 hypothetical protein DVU2718 233, 263
DVU2745 hypothetical protein DVU2745 263, 309
DVU2778 hypothetical protein DVU2778 215, 263
DVUA0028 hypothetical protein DVUA0028 175, 263
DVUA0074 sulfotransferase family protein 98, 288
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 DVU1690
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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