Organism : Pseudomonas aeruginosa | Module List :
PA4602 glyA3

serine hydroxymethyltransferase (NCBI)

CircVis
Functional Annotations (12)
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
Cyanoamino acid 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 PA4602
(Mouseover regulator name to see its description)

PA4602 is regulated by 53 influences and regulates 0 modules.
Regulators for PA4602 glyA3 (53)
Regulator Module Operator
PA0167 106 tf
PA0393 106 tf
PA0701 106 tf
PA0815 106 tf
PA1397 106 tf
PA1539 106 tf
PA1898 106 tf
PA2196 106 tf
PA2622 106 tf
PA2665 106 tf
PA2696 106 tf
PA2899 106 tf
PA2957 106 tf
PA3002 106 tf
PA3126 106 tf
PA3184 106 tf
PA3225 106 tf
PA3604 106 tf
PA4052 106 tf
PA4269 106 tf
PA4270 106 tf
PA4275 106 tf
PA4451 106 tf
PA4745 106 tf
PA4890 106 tf
PA5166 106 tf
PA5324 106 tf
PA0155 433 tf
PA0275 433 tf
PA0393 433 tf
PA0576 433 tf
PA0873 433 tf
PA0905 433 tf
PA1539 433 tf
PA1759 433 tf
PA1898 433 tf
PA1945 433 tf
PA3002 433 tf
PA3007 433 tf
PA3027 433 tf
PA3215 433 tf
PA3604 433 tf
PA3965 433 tf
PA4070 433 tf
PA4120 433 tf
PA4238 433 tf
PA4341 433 tf
PA4600 433 tf
PA4745 433 tf
PA4755 433 tf
PA4853 433 tf
PA5344 433 tf
PA5525 433 tf

Warning: PA4602 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
3044 3.10e-01 GaTcgTTcAcaaaAcTttGC
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3045 1.50e+00 tgTAG.AtacgCgcc
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3686 1.50e+03 ggTTgct..tCgcAa.aCtat
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3687 1.30e+00 gGctAtaATGtccccCcTTtTTT
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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 PA4602

PA4602 is enriched for 12 functions in 3 categories.
Enrichment Table (12)
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
Cyanoamino acid 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 PA4602

PA4602 has total of 29 gene neighbors in modules 106, 433
Gene neighbors (29)
Gene Common Name Description Module membership
PA0009 glyQ glycyl-tRNA synthetase alpha subunit (NCBI) 106, 453
PA0316 serA D-3-phosphoglycerate dehydrogenase (NCBI) 106, 433
PA0420 bioA adenosylmethionine--8-amino-7-oxononanoate transaminase (NCBI) 78, 433
PA0548 tktA transketolase (NCBI) 433, 436
PA0576 rpoD sigma factor RpoD (NCBI) 186, 433
PA0956 proS prolyl-tRNA synthetase (NCBI) 214, 433
PA1794 glnS glutaminyl-tRNA synthetase (NCBI) 426, 433
PA1796 folD 5,10-methylene-tetrahydrofolate dehydrogenase / cyclohydrolase (NCBI) 106, 544
PA2629 purB adenylosuccinate lyase (NCBI) 106, 544
PA3001 PA3001 glyceraldehyde-3-phosphate dehydrogenase (NCBI) 186, 433
PA3637 pyrG CTP synthetase (NCBI) 198, 433
PA3654 pyrH uridylate kinase (NCBI) 106, 453
PA3763 purL phosphoribosylformylglycinamidine synthase (NCBI) 106, 204
PA3770 guaB inositol-5-monophosphate dehydrogenase (NCBI) 90, 106
PA3976 thiE thiamine-phosphate diphosphorylase (NCBI) 106, 286
PA4333 PA4333 probable fumarase (NCBI) 90, 433
PA4560 ileS isoleucyl-tRNA synthetase (NCBI) 43, 106
PA4602 glyA3 serine hydroxymethyltransferase (NCBI) 106, 433
PA4729 panB 3-methyl-2-oxobutanoate hydroxymethyltransferase (NCBI) 329, 433
PA4730 panC pantoate--beta-alanine ligase (NCBI) 329, 433
PA4758 carA carbamoyl-phosphate synthase small subunit (NCBI) 106, 453
PA4888 PA4888 hypothetical protein (NCBI) 106, 332
PA4889 PA4889 probable oxidoreductase (NCBI) 106, 332
PA4890 PA4890 hypothetical protein (NCBI) 106, 332
PA4956 rhdA thiosulfate sulfurtransferase (NCBI) 286, 433
PA4957 psd phosphatidylserine decarboxylase (NCBI) 286, 433
PA5063 ubiE ubiquinone/menaquinone biosynthesis methyltransferase (NCBI) 223, 433
PA5064 PA5064 hypothetical protein (NCBI) 214, 433
PA5296 rep ATP-dependent DNA helicase Rep (NCBI) 106, 230
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 PA4602
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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