Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1203 glyA

serine hydroxymethyltransferase

CircVis
Functional Annotations (11)
Function System
Glycine/serine hydroxymethyltransferase cog/ cog
glycine hydroxymethyltransferase activity go/ molecular_function
glycine metabolic process go/ biological_process
L-serine metabolic process go/ biological_process
pyridoxal phosphate binding go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
One carbon pool by folate kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1203
(Mouseover regulator name to see its description)

DVU1203 is regulated by 26 influences and regulates 0 modules.
Regulators for DVU1203 glyA (26)
Regulator Module Operator
DVU0619
DVU3381
248 combiner
DVU0629 248 tf
DVU0653
DVU2275
248 combiner
DVU0744
DVU2690
248 combiner
DVU1402 248 tf
DVU1547 248 tf
DVU1744 248 tf
DVU1788
DVU2275
248 combiner
DVU2086
DVU0619
248 combiner
DVU2532
DVU1788
248 combiner
DVU2547
DVU1628
248 combiner
DVU2547
DVU2644
248 combiner
DVU2557 248 tf
DVU2644 248 tf
DVU3142 248 tf
DVU3167
DVU1690
248 combiner
DVU3167
DVU1949
248 combiner
DVUA0024 248 tf
DVU0619
DVU0525
169 combiner
DVU0619
DVU3381
169 combiner
DVU0744
DVU0230
169 combiner
DVU1518
DVU2086
169 combiner
DVU2086
DVU2832
169 combiner
DVU2532
DVU0653
169 combiner
DVU3167
DVU0063
169 combiner
DVU3167
DVU1572
169 combiner

Warning: DVU1203 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
323 9.00e-06 AAGaGaatGagGtcTtaTaCC
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RegPredict
324 2.90e-04 aAcctGTGCaggGctggcGAcAtg
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RegPredict
473 2.30e+02 TTtTcCG
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RegPredict
474 4.60e+03 agTatcTT
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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 DVU1203

DVU1203 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
Glycine/serine hydroxymethyltransferase cog/ cog
glycine hydroxymethyltransferase activity go/ molecular_function
glycine metabolic process go/ biological_process
L-serine metabolic process go/ biological_process
pyridoxal phosphate binding go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
One carbon pool by folate kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Module neighborhood information for DVU1203

DVU1203 has total of 39 gene neighbors in modules 169, 248
Gene neighbors (39)
Gene Common Name Description Module membership
DVU1002 hypothetical protein DVU1002 169, 172
DVU1003 dnaJ domain-containing protein 169, 172
DVU1194 hypothetical protein DVU1194 169, 308
DVU1195 lipoprotein 29, 169
DVU1196 leuS leucyl-tRNA synthetase 65, 169
DVU1197 nusB N utilization substance protein B 65, 248
DVU1198 ribH 6,7-dimethyl-8-ribityllumazine synthase 169, 248
DVU1199 ribAB 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II 248, 292
DVU1200 ribE riboflavin synthase subunit alpha 169, 308
DVU1201 ribD riboflavin biosynthesis protein RibD 94, 169
DVU1202 cytidine/deoxycytidylate deaminase family protein 10, 169
DVU1203 glyA serine hydroxymethyltransferase 169, 248
DVU1204 fabF 3-oxoacyl-ACP synthase 169, 248
DVU1205 acpP acyl carrier protein 169, 323
DVU1206 fabG 3-oxoacyl-ACP reductase 169, 323
DVU1207 fabH 3-oxoacyl-ACP synthase 10, 169
DVU1209 rpmF 50S ribosomal protein L32 169, 308
DVU1210 hypothetical protein DVU1210 28, 169
DVU1211 rpmB 50S ribosomal protein L28 169, 308
DVU1304 rplD 50S ribosomal protein L4 212, 248
DVU1305 rplW 50S ribosomal protein L23 212, 248
DVU1306 rplB 50S ribosomal protein L2 212, 248
DVU1307 rpsS 30S ribosomal protein S19 212, 248
DVU1314 rplX 50S ribosomal protein L24 248, 292
DVU1315 rplE 50S ribosomal protein L5 212, 248
DVU1321 rpmD 50S ribosomal protein L30 212, 248
DVU1322 rplO 50S ribosomal protein L15 212, 248
DVU1623 pyrG CTP synthetase 248, 292
DVU1780 hypothetical protein DVU1780 169, 229
DVU1781 hypothetical protein DVU1781 169, 229
DVU1782 iron-sulfur cluster-binding protein 169, 229
DVU1783 hypothetical protein DVU1783 169, 229
DVU1784 short chain dehydrogenase/reductase family oxidoreductase 169, 229
DVU1785 MarC membrane protein 169, 229
DVU1891 hypothetical protein DVU1891 27, 169
DVU2226 acetyl-CoA carboxylase, biotin carboxylase 248, 292
DVU2929 rpoC DNA-directed RNA polymerase subunit beta' 151, 248
DVU3176 UDP-glucose/GDP-mannose dehydrogenase family protein 169, 292
DVU3177 hypothetical protein DVU3177 145, 169
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 DVU1203
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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