Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0813 hrcA

heat-inducible transcription repressor HrcA

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator of heat shock gene cog/ cog
regulation of transcription, DNA-dependent go/ biological_process
hrcA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0813
(Mouseover regulator name to see its description)

DVU0813 is regulated by 26 influences and regulates 34 modules.
Regulators for DVU0813 hrcA (26)
Regulator Module Operator
DVU0916 287 tf
DVU0936
DVU0269
287 combiner
DVU1518
DVU2086
287 combiner
DVU1584 287 tf
DVU1788 287 tf
DVU2086 287 tf
DVU2086
DVU0744
287 combiner
DVU2086
DVU1788
287 combiner
DVU2086
DVU2819
287 combiner
DVU2547 287 tf
DVU2547
DVU0230
287 combiner
DVU2547
DVU2086
287 combiner
DVU2909
DVU1730
287 combiner
DVU3255
DVU1584
287 combiner
DVU0744
DVU0525
209 combiner
DVU0946
DVU0269
209 combiner
DVU1584 209 tf
DVU1628 209 tf
DVU1690
DVU0269
209 combiner
DVU1788 209 tf
DVU2547
DVU0230
209 combiner
DVU2547
DVU1628
209 combiner
DVU2909
DVU1730
209 combiner
DVU3255
DVU1584
209 combiner
DVU3255
DVU1690
209 combiner
DVUA0057
DVU1730
209 combiner

Warning: DVU0813 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
399 5.30e+03 aTGaCaAg
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RegPredict
400 5.10e+03 GtCTTatCttAaaGgcaGA
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RegPredict
549 2.90e+03 gtGgcTtatc..A.aGg.aGA
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RegPredict
550 1.30e+04 ttAT..Tt.TcAGGAggAA
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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 DVU0813

DVU0813 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator of heat shock gene cog/ cog
regulation of transcription, DNA-dependent go/ biological_process
hrcA tigr/ tigrfam
Module neighborhood information for DVU0813

DVU0813 has total of 15 gene neighbors in modules 209, 287
Gene neighbors (15)
Gene Common Name Description Module membership
DVU0419 nspC carboxynorspermidine decarboxylase 173, 287
DVU0572 hypothetical protein DVU0572 209, 287
DVU0576 msrB methionine sulfoxide reductase B 173, 209
DVU0665 nitrogen fixation protein nifU 209, 218
DVU0813 hrcA heat-inducible transcription repressor HrcA 209, 287
DVU1457 thioredoxin reductase 209, 287
DVU1601 ATP-dependent Clp protease adaptor protein ClpS 209, 287
DVU1875 dafA protein 209, 287
DVU1876 dnaJ protein 209, 287
DVU1984 msrA peptide methionine sulfoxide reductase MsrA 209, 287
DVU2086 GntR family transcriptional regulator 209, 267
DVU2325 merP mercuric transport protein periplasmic component 209, 287
DVU2497 lipoprotein 209, 287
DVU2893 flagellar basal-body rod protein 209, 287
DVU2975 hydrolase 173, 287
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 DVU0813
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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