Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1653

polyA polymerase family protein

CircVis
Functional Annotations (6)
Function System
tRNA nucleotidyltransferase/poly(A) polymerase cog/ cog
RNA binding go/ molecular_function
RNA processing go/ biological_process
nucleotidyltransferase activity go/ molecular_function
hydrolase activity go/ molecular_function
manganese ion binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1653
(Mouseover regulator name to see its description)

DVU1653 is regulated by 17 influences and regulates 0 modules.
Regulators for DVU1653 (17)
Regulator Module Operator
DVU2106
DVU2251
196 combiner
DVU2251
DVU3066
196 combiner
DVU2989 196 tf
DVU0230 220 tf
DVU0309
DVU0653
220 combiner
DVU0569 220 tf
DVU0653
DVU2251
220 combiner
DVU0653
DVU3305
220 combiner
DVU1518
DVU1561
220 combiner
DVU1561 220 tf
DVU1759 220 tf
DVU2359
DVU0230
220 combiner
DVU2532
DVU0653
220 combiner
DVU3167
DVU0309
220 combiner
DVU3167
DVU0936
220 combiner
DVU3167
DVUA0100
220 combiner
DVU3313
DVU0230
220 combiner

Warning: DVU1653 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
375 2.40e+01 aa..tcaa...Ttgcac.aaAaaa
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RegPredict
376 2.10e+02 TTccacatcaa
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RegPredict
419 1.10e+02 Ctat.c.tTt.CgTTgct
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RegPredict
420 6.00e+02 GcCctCGTGcgGC.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 DVU1653

DVU1653 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
tRNA nucleotidyltransferase/poly(A) polymerase cog/ cog
RNA binding go/ molecular_function
RNA processing go/ biological_process
nucleotidyltransferase activity go/ molecular_function
hydrolase activity go/ molecular_function
manganese ion binding go/ molecular_function
Module neighborhood information for DVU1653

DVU1653 has total of 42 gene neighbors in modules 196, 220
Gene neighbors (42)
Gene Common Name Description Module membership
DVU1094 argH argininosuccinate lyase 220, 251
DVU1095 argG argininosuccinate synthase 220, 262
DVU1408 hypothetical protein DVU1408 63, 196
DVU1653 polyA polymerase family protein 196, 220
DVU1913 aspartate kinase 220, 250
DVU1914 alpha-isopropylmalate/homocitrate synthase family transferase 172, 196
DVU1985 hypothetical protein DVU1985 196, 226
DVU1990 hypothetical protein DVU1990 146, 196
DVU2001 None 90, 220
DVU2009 hypothetical protein DVU2009 196, 273
DVU2012 hypothetical protein DVU2012 196, 273
DVU2015 hypothetical protein DVU2015 196, 273
DVU2016 GGDEF domain-containing protein 196, 273
DVU2027 hypothetical protein DVU2027 196, 273
DVU2032 ERF family protein 196, 344
DVU2034 hypothetical protein DVU2034 196, 273
DVU2038 hypothetical protein DVU2038 196, 273
DVU2044 hypothetical protein DVU2044 167, 196
DVU2045 hypothetical protein DVU2045 196, 273
DVU2047 hypothetical protein DVU2047 196, 273
DVU2049 None 196, 337
DVU2057 hypothetical protein DVU2057 196, 217
DVU2087 hypothetical protein DVU2087 33, 196
DVU2089 hypothetical protein DVU2089 66, 196
DVU3024 hypothetical protein DVU3024 207, 220
DVU3025 poR pyruvate-ferredoxin oxidoreductase 207, 220
DVU3026 L-lactate permease family protein 139, 220
DVU3027 glcD glycolate oxidase subunit GlcD 207, 220
DVU3028 iron-sulfur cluster-binding protein 139, 220
DVU3029 pta phosphate acetyltransferase 207, 220
DVU3030 ackA acetate kinase 207, 220
DVU3031 hypothetical protein DVU3031 207, 220
DVU3032 hypothetical protein DVU3032 207, 220
DVU3033 iron-sulfur cluster-binding protein 139, 220
DVU3197 ilvE branched-chain amino acid aminotransferase 220, 249
DVU3199 hypothetical protein DVU3199 23, 220
DVU3200 recR recombination protein RecR 23, 220
DVU3235 IMP cyclohydrolase 81, 220
DVU3347 pyruvate ferredoxin/flavodoxin oxidoreductase family protein 81, 220
DVU3348 pyruvate ferredoxin/flavodoxin oxidoreductase subunit beta 220, 250
DVU3349 2-ketoisovalerate ferredoxin reductase 220, 250
DVU3350 iron-sulfur cluster-binding protein 220, 250
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 DVU1653
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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