Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1336 clpX

ATP-dependent protease ATP-binding subunit ClpX

CircVis
Functional Annotations (12)
Function System
ATP-dependent protease Clp, ATPase subunit cog/ cog
ATP binding go/ molecular_function
DNA repair go/ biological_process
DNA recombination go/ biological_process
zinc ion binding go/ molecular_function
endopeptidase Clp activity go/ molecular_function
four-way junction helicase activity go/ molecular_function
protein transport go/ biological_process
ATPase activity go/ molecular_function
protein metabolic process go/ biological_process
protein dimerization activity go/ molecular_function
clpX tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1336
(Mouseover regulator name to see its description)

DVU1336 is regulated by 27 influences and regulates 0 modules.
Regulators for DVU1336 clpX (27)
Regulator Module Operator
DVU0813
DVU0230
158 combiner
DVU0936 158 tf
DVU1628
DVU0813
158 combiner
DVU1690 158 tf
DVU1788 158 tf
DVU1788
DVU2690
158 combiner
DVU2086
DVU0744
158 combiner
DVU2086
DVU2909
158 combiner
DVU2547 158 tf
DVU2547
DVU1788
158 combiner
DVU2547
DVU2086
158 combiner
DVU3255 158 tf
DVUA0151
DVU1788
158 combiner
DVU0525 120 tf
DVU0619
DVU0525
120 combiner
DVU0813 120 tf
DVU0813
DVU0230
120 combiner
DVU0813
DVU1745
120 combiner
DVU0854 120 tf
DVU1628 120 tf
DVU1645 120 tf
DVU1690 120 tf
DVU1730 120 tf
DVU1788 120 tf
DVU2086
DVU0744
120 combiner
DVU2547 120 tf
DVU2686 120 tf

Warning: DVU1336 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
231 2.90e+03 GgtTGACaacg
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RegPredict
232 1.60e+04 AGgGGGgAGactCG
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RegPredict
301 2.70e+03 tCCtGTTG
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RegPredict
302 2.90e+03 gATcAcGCc.CaCgtCaacGAtGc
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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 DVU1336

DVU1336 is enriched for 12 functions in 3 categories.
Enrichment Table (12)
Function System
ATP-dependent protease Clp, ATPase subunit cog/ cog
ATP binding go/ molecular_function
DNA repair go/ biological_process
DNA recombination go/ biological_process
zinc ion binding go/ molecular_function
endopeptidase Clp activity go/ molecular_function
four-way junction helicase activity go/ molecular_function
protein transport go/ biological_process
ATPase activity go/ molecular_function
protein metabolic process go/ biological_process
protein dimerization activity go/ molecular_function
clpX tigr/ tigrfam
Module neighborhood information for DVU1336

DVU1336 has total of 25 gene neighbors in modules 120, 158
Gene neighbors (25)
Gene Common Name Description Module membership
DVU0242 SecC motif-containing protein 114, 158
DVU0298 hypothetical protein DVU0298 110, 120
DVU0370 hypothetical protein DVU0370 120, 281
DVU0421 agmatinase 110, 120
DVU0526 drug resistance transporter 90, 120
DVU0590 hypothetical protein DVU0590 46, 120
DVU0662 cysE serine O-acetyltransferase 4, 120
DVU0664 cysteine desulfurase 4, 120
DVU0758 hypothetical protein DVU0758 120, 158
DVU0857 radical SAM domain-containing protein 158, 218
DVU0865 membrane-associated zinc metalloprotease 158, 227
DVU0994 hypothetical protein DVU0994 158, 218
DVU1212 fsxA fxsA protein 4, 120
DVU1213 rhomboid family protein 69, 120
DVU1267 hypothetical protein DVU1267 158, 227
DVU1278 ftsH cell division protein FtsH 120, 158
DVU1336 clpX ATP-dependent protease ATP-binding subunit ClpX 120, 158
DVU1337 lon ATP-dependent protease La 114, 158
DVU1602 clpA ATP-dependent Clp protease, ATP-binding subunit ClpA 158, 193
DVU1874 clpB ATP-dependent Clp protease, ATP-binding subunit ClpB 4, 158
DVU2310 metallo-beta-lactamase family protein 104, 158
DVU2470 membrane protein 158, 194
DVU2555 MATE efflux family protein 119, 120
DVU3345 None 63, 120
DVU3346 hypothetical protein DVU3346 120, 167
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 DVU1336
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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