Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0071 dinP

DNA polymerase IV

CircVis
Functional Annotations (16)
Function System
Nucleotidyltransferase/DNA polymerase involved in DNA repair cog/ cog
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA repair go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0071
(Mouseover regulator name to see its description)

DVU0071 is regulated by 15 influences and regulates 0 modules.
Regulators for DVU0071 dinP (15)
Regulator Module Operator
DVU1063 161 tf
DVU1402
DVU1340
161 combiner
DVU1690
DVUA0143
161 combiner
DVU2557 161 tf
DVU2557
DVU1156
161 combiner
DVU2633 161 tf
DVU2909
DVU1690
161 combiner
DVU2909
DVU2527
161 combiner
DVUA0143
DVU1745
161 combiner
DVUA0151
DVU0936
161 combiner
DVU1517 162 tf
DVU2588
DVU0529
162 combiner
DVU2785
DVU0230
162 combiner
DVU3255
DVU0110
162 combiner
DVUA0057
DVU0529
162 combiner

Warning: DVU0071 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
307 1.60e+03 tC.gcTGTCAtccCg
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RegPredict
308 2.40e+04 aTGtgtcGc.CatGg
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RegPredict
309 8.80e+01 CG.aagaCatgACA
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RegPredict
310 3.60e+03 CTgCc.gATGg
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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 DVU0071

DVU0071 is enriched for 16 functions in 3 categories.
Enrichment Table (16)
Function System
Nucleotidyltransferase/DNA polymerase involved in DNA repair cog/ cog
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA repair go/ biological_process
Module neighborhood information for DVU0071

DVU0071 has total of 55 gene neighbors in modules 161, 162
Gene neighbors (55)
Gene Common Name Description Module membership
DVU0029 hydantoinase/oxoprolinase family protein 162, 185
DVU0038 acyltransferase domain-containing protein 69, 161
DVU0071 dinP DNA polymerase IV 161, 162
DVU0077 hypothetical protein DVU0077 87, 162
DVU0080 fumC fumarate hydratase 14, 162
DVU0089 hypothetical protein DVU0089 161, 245
DVU0104 cation ABC transporter permease 69, 162
DVU0127 hypothetical protein DVU0127 162, 316
DVU0154 hypothetical protein DVU0154 162, 334
DVU0184 hypothetical protein DVU0184 162, 337
DVU0194 terminase large subunit 162, 334
DVU0213 hypothetical protein DVU0213 161, 314
DVU0291 ABC transporter ATP-binding protein 35, 162
DVU0292 hypothetical protein DVU0292 162, 185
DVU0295 amine oxidase, flavin-containing 87, 162
DVU0332 hypothetical protein DVU0332 89, 161
DVU0346 hypothetical protein DVU0346 162, 181
DVU0347 hexapaptide repeat-containing transferase 55, 162
DVU0391 hypothetical protein DVU0391 99, 161
DVU0435 hypothetical protein DVU0435 161, 238
DVU0455 hypothetical protein DVU0455 161, 179
DVU0485 hypothetical protein DVU0485 161, 277
DVU0540 sensor histidine kinase 162, 198
DVU0569 sigma-54 dependent transcriptional regulator 162, 174
DVU0585 hypothetical protein DVU0585 126, 162
DVU0740 hypothetical protein DVU0740 87, 162
DVU0804 sigma-54 dependent transcriptional regulator/response regulator 161, 260
DVU0844 None 126, 162
DVU0859 hypothetical protein DVU0859 69, 162
DVU0907 hypothetical protein DVU0907 162, 277
DVU0971 molybdenum cofactor biosynthesis protein 17, 161
DVU1100 tail fiber protein 12, 161
DVU1159 hypothetical protein DVU1159 161, 175
DVU1160 urea transporter 161, 185
DVU1389 hypothetical protein DVU1389 69, 162
DVU1566 phosphoadenosine phosphosulfate reductase 161, 225
DVU2092 thiamine biosynthesis protein ThiF 161, 304
DVU2123 hypothetical protein DVU2123 161, 321
DVU2124 hypothetical protein DVU2124 161, 321
DVU2315 hypothetical protein DVU2315 162, 176
DVU2361 hypothetical protein DVU2361 161, 198
DVU2462 oligopeptide ABC transporter permease 17, 161
DVU2544 iron-sulfur cluster-binding protein 153, 161
DVU2619 hypothetical protein DVU2619 145, 162
DVU2629 hypothetical protein DVU2629 161, 238
DVU2834 hypothetical protein DVU2834 161, 245
DVU2866 hypothetical protein DVU2866 162, 204
DVU2867 holin 162, 204
DVU2883 selA selenocysteine synthase 62, 162
DVU2970 acetyltransferase 162, 285
DVU3013 glycosyl transferase group 2 family protein 162, 174
DVU3022 sensory box histidine kinase/response regulator 162, 174
DVU3195 lipoprotein 161, 214
DVU3203 DNA polymerase III subunit delta' 161, 316
DVU3335 sensory box histidine kinase 162, 249
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 DVU0071
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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