Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3256 mutM

formamidopyrimidine-DNA glycosylase

CircVis
Functional Annotations (8)
Function System
Formamidopyrimidine-DNA glycosylase cog/ cog
damaged DNA binding go/ molecular_function
base-excision repair go/ biological_process
nucleotide-excision repair go/ biological_process
zinc ion binding go/ molecular_function
oxidized purine base lesion DNA N-glycosylase activity go/ molecular_function
Base excision repair kegg/ kegg pathway
fpg tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU3256
(Mouseover regulator name to see its description)

DVU3256 is regulated by 16 influences and regulates 0 modules.
Regulators for DVU3256 mutM (16)
Regulator Module Operator
DVU0057 238 tf
DVU0653
DVU2251
238 combiner
DVU0936
DVU0653
238 combiner
DVU1754
DVU3334
238 combiner
DVU2111
DVU1517
238 combiner
DVU2788
DVU0936
238 combiner
DVU2886
DVU0525
238 combiner
DVU0057
DVU0539
320 combiner
DVU0606 320 tf
DVU0653
DVU2633
320 combiner
DVU1584
DVU1744
320 combiner
DVU1745 320 tf
DVU2633 320 tf
DVU2832 320 tf
DVU2886
DVUA0057
320 combiner
DVU3080
DVU2960
320 combiner

Warning: DVU3256 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
455 1.20e+02 GcGCGAcgTGTgccgggccatGTG
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RegPredict
456 5.60e+02 GgATgccgtcT
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RegPredict
609 5.90e+04 AAAACcTCAACA
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RegPredict
610 3.60e+04 GAAAGCaTACtttC
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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 DVU3256

DVU3256 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Formamidopyrimidine-DNA glycosylase cog/ cog
damaged DNA binding go/ molecular_function
base-excision repair go/ biological_process
nucleotide-excision repair go/ biological_process
zinc ion binding go/ molecular_function
oxidized purine base lesion DNA N-glycosylase activity go/ molecular_function
Base excision repair kegg/ kegg pathway
fpg tigr/ tigrfam
Module neighborhood information for DVU3256

DVU3256 has total of 31 gene neighbors in modules 238, 320
Gene neighbors (31)
Gene Common Name Description Module membership
DVU0010 TRAP transporter subunit DctQ 182, 238
DVU0011 TRAP transporter solute receptor DctP 238, 260
DVU0171 hemolysin-like protein 82, 238
DVU0179 fused molybdenum-pterin binding domain-containing protein/site-specific recombinase phage integrase family 26, 320
DVU0188 hypothetical protein DVU0188 106, 238
DVU0306 hypothetical protein DVU0306 320, 326
DVU0355 sensory box protein 222, 320
DVU0385 hypothetical protein DVU0385 91, 320
DVU0406 hypothetical protein DVU0406 127, 238
DVU0435 hypothetical protein DVU0435 161, 238
DVU0437 RND family efflux transporter MFP subunit 68, 238
DVU0457 EAL domain-containing protein 238, 322
DVU0568 tRNA 2-selenouridine synthase 51, 238
DVU0798 hypothetical protein DVU0798 225, 320
DVU1216 hypothetical protein DVU1216 238, 305
DVU1253 hypothetical protein DVU1253 25, 238
DVU1421 hypothetical protein DVU1421 68, 238
DVU1920 hypothetical protein DVU1920 109, 320
DVU2081 hypothetical protein DVU2081 238, 302
DVU2093 thiH thiamine biosynthesis protein ThiH 46, 238
DVU2242 asparaginase family protein 84, 238
DVU2321 hypothetical protein DVU2321 238, 316
DVU2610 hypothetical protein DVU2610 238, 316
DVU2629 hypothetical protein DVU2629 161, 238
DVU2918 hypothetical protein DVU2918 109, 238
DVU3063 mviN-2 integral membrane protein MviN 238, 305
DVU3256 mutM formamidopyrimidine-DNA glycosylase 238, 320
DVU3318 hypothetical protein DVU3318 313, 320
DVU3376 sulfatase family protein 238, 254
DVU3377 dgkA diacylglycerol kinase 25, 238
DVU3394 hypothetical protein DVU3394 25, 238
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 DVU3256
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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