Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1335 clpP

ATP-dependent Clp protease proteolytic subunit

CircVis
Functional Annotations (5)
Function System
Protease subunit of ATP-dependent Clp proteases cog/ cog
proteolysis go/ biological_process
endopeptidase Clp activity go/ molecular_function
endopeptidase Clp complex go/ cellular_component
clpP tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1335
(Mouseover regulator name to see its description)

DVU1335 is regulated by 22 influences and regulates 0 modules.
Regulators for DVU1335 clpP (22)
Regulator Module Operator
DVU1144 16 tf
DVU2086 16 tf
DVU2251 16 tf
DVU2686 16 tf
DVU2832 16 tf
DVU2836
DVU3084
16 combiner
DVU3080 16 tf
DVU3167
DVU0269
16 combiner
DVU3167
DVU2114
16 combiner
DVU3167
DVU2532
16 combiner
DVU3186
DVU0269
16 combiner
DVU1156 308 tf
DVU1331
DVU0916
308 combiner
DVU1572 308 tf
DVU1572
DVU2114
308 combiner
DVU2114 308 tf
DVU2675
DVU3186
308 combiner
DVU2799 308 tf
DVU3167
DVU1760
308 combiner
DVU3167
DVU2114
308 combiner
DVU3186 308 tf
DVU3255
DVU1144
308 combiner

Warning: DVU1335 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
31 4.60e-01 GaAaaGacAT
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RegPredict
32 1.20e+02 tTATCAcGccacaCaTCAAG
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RegPredict
589 9.70e-01 AtACCctgactgcGGAAAAtgCAA
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RegPredict
590 1.60e+02 CcCCgGgCA.GGc.T
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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 DVU1335

DVU1335 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Protease subunit of ATP-dependent Clp proteases cog/ cog
proteolysis go/ biological_process
endopeptidase Clp activity go/ molecular_function
endopeptidase Clp complex go/ cellular_component
clpP tigr/ tigrfam
Module neighborhood information for DVU1335

DVU1335 has total of 47 gene neighbors in modules 16, 308
Gene neighbors (47)
Gene Common Name Description Module membership
DVU0275 polysaccharide deacetylase family protein 71, 308
DVU0356 tag DNA-3-methyladenine glycosylase I 255, 308
DVU0407 rare lipoprotein A family protein 16, 229
DVU0448 gmd GDP-mannose 4,6-dehydratase 308, 341
DVU0916 redox-sensing transcriptional repressor Rex 8, 16
DVU0941 M16 family peptidase 16, 318
DVU1005 hypothetical protein DVU1005 16, 27
DVU1174 hypothetical protein DVU1174 27, 308
DVU1175 hypothetical protein DVU1175 143, 308
DVU1194 hypothetical protein DVU1194 169, 308
DVU1200 ribE riboflavin synthase subunit alpha 169, 308
DVU1209 rpmF 50S ribosomal protein L32 169, 308
DVU1211 rpmB 50S ribosomal protein L28 169, 308
DVU1244 hypothetical protein DVU1244 16, 71
DVU1335 clpP ATP-dependent Clp protease proteolytic subunit 16, 308
DVU1405 hypothetical protein DVU1405 229, 308
DVU1572 CarD family transcriptional regulator 16, 332
DVU1582 hypothetical protein DVU1582 16, 282
DVU1612 ACT domain-containing protein 16, 232
DVU1647 lysA-1 diaminopimelate decarboxylase 16, 128
DVU1648 lipoprotein 16, 128
DVU1649 mutS DNA mismatch repair protein MutS 16, 128
DVU1655 LL-diaminopimelate aminotransferase 16, 128
DVU1656 folK 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase 16, 71
DVU1742 prevent-host-death family protein 221, 308
DVU1850 CBS domain-containing protein 16, 30
DVU1851 M24/M37 family peptidase 5, 16
DVU1861 prfB peptide chain release factor 2, programmed frameshift 16, 308
DVU1867 dapF diaminopimelate epimerase 16, 71
DVU1923 hupD hydrogenase expression/formation protein HupD 229, 308
DVU2066 phage integrase family site specific recombinase 219, 308
DVU2104 iron-sulfur cluster-binding/ATPase 53, 308
DVU2201 iron-containing alcohol dehydrogenase 16, 308
DVU2216 infA translation initiation factor IF-1 235, 308
DVU2235 hypothetical protein DVU2235 215, 308
DVU2236 hypothetical protein DVU2236 245, 308
DVU2417 SlyX protein 268, 308
DVU2607 hypothetical protein DVU2607 88, 308
DVU2609 chemotaxis MotB protein 16, 135
DVU2650 hypothetical protein DVU2650 16, 88
DVU2655 D-alanyl-D-alanine carboxypeptidase 16, 143
DVU2980 pssA CDP-diacylglycerol--serine O-phosphatidyltransferase 145, 308
DVU3061 sensory box histidine kinase 55, 308
DVU3117 hypothetical protein DVU3117 308, 332
DVU3146 hypothetical protein DVU3146 219, 308
DVU3191 rluC ribosomal large subunit pseudouridine synthase C 52, 308
DVUA0071 glycosyl transferase, group 1/2 family protein 16, 121
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 DVU1335
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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