Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1424 gcvPB

glycine dehydrogenase subunit 2

CircVis
Functional Annotations (8)
Function System
Glycine cleavage system protein P (pyridoxal-binding), C-terminal domain cog/ cog
glycine cleavage system go/ molecular_function
glycine dehydrogenase (decarboxylating) activity go/ molecular_function
glycine cleavage complex go/ cellular_component
glycine metabolic process go/ biological_process
pyridoxal phosphate binding go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1424
(Mouseover regulator name to see its description)

DVU1424 is regulated by 25 influences and regulates 0 modules.
Regulators for DVU1424 gcvPB (25)
Regulator Module Operator
DVU0110 250 tf
DVU0110
DVU0569
250 combiner
DVU0277 250 tf
DVU0309
DVU0110
250 combiner
DVU0309
DVU0653
250 combiner
DVU0653 250 tf
DVU0653
DVU2251
250 combiner
DVU1518
DVU0030
250 combiner
DVU1518
DVU1561
250 combiner
DVU1561
DVU0230
250 combiner
DVU1759 250 tf
DVU3167 250 tf
DVU3167
DVU0569
250 combiner
DVU3313 250 tf
DVU0277
DVU0309
180 combiner
DVU0309
DVU0110
180 combiner
DVU0569 180 tf
DVU1518
DVU1561
180 combiner
DVU1561 180 tf
DVU1561
DVU0230
180 combiner
DVU1561
DVUA0024
180 combiner
DVU2036
DVU0110
180 combiner
DVU3023 180 tf
DVU3023
DVU0110
180 combiner
DVU3023
DVU0569
180 combiner

Warning: DVU1424 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
343 8.10e+02 c.cgacGCcG.Acgc
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RegPredict
344 2.60e+04 gccC.gcCatcaCga
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RegPredict
477 1.20e+03 gTgCgGcgt.g.a.caac.a.cg
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RegPredict
478 1.50e+04 ctTgcCacggaAgGG
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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 DVU1424

DVU1424 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Glycine cleavage system protein P (pyridoxal-binding), C-terminal domain cog/ cog
glycine cleavage system go/ molecular_function
glycine dehydrogenase (decarboxylating) activity go/ molecular_function
glycine cleavage complex go/ cellular_component
glycine metabolic process go/ biological_process
pyridoxal phosphate binding go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for DVU1424

DVU1424 has total of 44 gene neighbors in modules 180, 250
Gene neighbors (44)
Gene Common Name Description Module membership
DVU0142 trpS tryptophanyl-tRNA synthetase 9, 180
DVU0169 oligopeptide/dipeptide ABC transporter periplasmic oligopeptide/dipeptide-binding protein 174, 250
DVU0255 hypothetical protein DVU0255 172, 250
DVU0326 hypE hydrogenase expression/formation protein HypE 117, 250
DVU0337 hypothetical protein DVU0337 81, 250
DVU0338 HAD superfamily hydrolase 180, 250
DVU0342 NAD-dependent epimerase/dehydratase family protein 81, 250
DVU0343 HPCH/HPAI aldolase family protein 81, 250
DVU0348 hypothetical protein DVU0348 23, 250
DVU0349 NeuB family protein 62, 250
DVU0350 spsF spore coat polysaccharide biosynthesis protein spsF 180, 250
DVU0353 iron-containing alcohol dehydrogenase 180, 250
DVU0492 argC N-acetyl-gamma-glutamyl-phosphate reductase 172, 250
DVU0495 hypothetical protein DVU0495 172, 180
DVU0653 sigma-54 dependent transcriptional regulator /response regulator 126, 180
DVU1039 lipoprotein 23, 180
DVU1040 hisB imidazoleglycerol-phosphate dehydratase 23, 180
DVU1185 colicin V production family protein 9, 180
DVU1252 hypothetical protein DVU1252 150, 250
DVU1424 gcvPB glycine dehydrogenase subunit 2 180, 250
DVU1426 gcvH glycine cleavage system protein H 176, 250
DVU1772 pyridine nucleotide-disulfide oxidoreductase 250, 327
DVU1913 aspartate kinase 220, 250
DVU1927 ileS isoleucyl-tRNA synthetase 23, 180
DVU1945 2-oxoglutarate ferredoxin oxidoreductase subunit alpha 250, 337
DVU1946 2-oxoglutarate ferredoxin oxidoreductase subunit beta 250, 337
DVU2210 hypothetical protein 180, 223
DVU2530 tkt transketolase 81, 250
DVU2575 M20/M25/M40 family peptidase 180, 277
DVU2757 radical SAM domain-containing protein 180, 327
DVU2892 GTP cyclohydrolase 180, 223
DVU2942 purB adenylosuccinate lyase 180, 327
DVU2951 glnS glutaminyl-tRNA synthetase 180, 250
DVU3006 polysaccharide biosynthesis protein/methyltransferase 22, 180
DVU3154 deoxyribonucleotide triphosphate pyrophosphatase 23, 250
DVU3157 hypothetical protein DVU3157 145, 250
DVU3167 heme biosynthesis protein 180, 327
DVU3198 DNA polymerase III subunits gamma/tau 23, 180
DVU3215 response regulator 87, 250
DVU3348 pyruvate ferredoxin/flavodoxin oxidoreductase subunit beta 220, 250
DVU3349 2-ketoisovalerate ferredoxin reductase 220, 250
DVU3350 iron-sulfur cluster-binding protein 220, 250
DVU3373 ilvD dihydroxy-acid dehydratase 81, 250
DVU3374 permease 81, 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 DVU1424
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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