Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3257

DNA internalization-related competence protein ComEC/Rec2

CircVis
Functional Annotations (2)
Function System
Predicted hydrolase (metallo-beta-lactamase superfamily) cog/ cog
hydrolase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU3257
(Mouseover regulator name to see its description)

DVU3257 is regulated by 24 influences and regulates 0 modules.
Regulators for DVU3257 (24)
Regulator Module Operator
DVU0230
DVU0621
193 combiner
DVU0539 193 tf
DVU0653 193 tf
DVU0946
DVU2114
193 combiner
DVU1063 193 tf
DVU2114 193 tf
DVU2532
DVU0946
193 combiner
DVU2567 193 tf
DVU2633 193 tf
DVU2909
DVU2588
193 combiner
DVU2960
DVU0916
193 combiner
DVU3142 193 tf
DVU3142
DVU0813
193 combiner
DVU0525 124 tf
DVU0539 124 tf
DVU0804
DVU3142
124 combiner
DVU1063 124 tf
DVU1754 124 tf
DVU1754
DVU1561
124 combiner
DVU2567 124 tf
DVU2588 124 tf
DVU2588
DVU0621
124 combiner
DVU3142
DVU1083
124 combiner
DVU3193
DVU2114
124 combiner

Warning: DVU3257 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
239 1.00e+01 CgACAGGagAc
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RegPredict
240 6.20e+03 CGgcCCtTCcc
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RegPredict
369 3.70e+03 GaCaAcacgccGtAA
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RegPredict
370 6.00e+02 G.CGACagG.gCAacGCAacA
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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 DVU3257

DVU3257 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted hydrolase (metallo-beta-lactamase superfamily) cog/ cog
hydrolase activity go/ molecular_function
Module neighborhood information for DVU3257

DVU3257 has total of 32 gene neighbors in modules 124, 193
Gene neighbors (32)
Gene Common Name Description Module membership
DVU0069 hypothetical protein DVU0069 193, 201
DVU0316 flgB flagellar basal body rod protein FlgB 36, 193
DVU0430 ech hydrogenase subunit EchE 85, 124
DVU0488 purD phosphoribosylamine--glycine ligase 193, 326
DVU0494 class V aminotransferase 36, 193
DVU0514 FlgA family protein 36, 193
DVU0658 HSP20 family protein 124, 217
DVU0668 methyl-accepting chemotaxis protein 193, 270
DVU0894 aroC chorismate synthase 32, 124
DVU1052 CBS domain-containing protein 102, 124
DVU1208 plsX glycerol-3-phosphate acyltransferase PlsX 28, 124
DVU1602 clpA ATP-dependent Clp protease, ATP-binding subunit ClpA 158, 193
DVU1766 aspartate ammonia-lyase 124, 261
DVU1940 anaerobic glycerol-3-phosphate dehydrogenase subunit A 36, 193
DVU1941 HAD family hydrolase 86, 193
DVU1957 hypothetical protein DVU1957 3, 193
DVU2139 histone deacetylase family protein 1, 124
DVU2217 acetyltransferase 193, 213
DVU2326 hypothetical protein DVU2326 1, 193
DVU2549 hypothetical protein DVU2549 193, 201
DVU2550 hypothetical protein DVU2550 193, 201
DVU2601 None 124, 168
DVU2640 hypothetical protein DVU2640 86, 124
DVU2758 hypothetical protein DVU2758 124, 345
DVU2777 hypothetical protein DVU2777 124, 295
DVU3082 methyl-accepting chemotaxis protein 193, 205
DVU3162 ABC transporter periplasmic substrate-binding protein 137, 193
DVU3169 cbiG cobalamin biosynthesis protein CbiG 19, 124
DVU3257 DNA internalization-related competence protein ComEC/Rec2 124, 193
DVU3387 hypothetical protein DVU3387 36, 193
DVUA0092 hypothetical protein DVUA0092 61, 193
DVUA0148 major facilitator superfamily protein 61, 124
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 DVU3257
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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