Organism : Pseudomonas aeruginosa | Module List :
PA5415 glyA1

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 PA5415
(Mouseover regulator name to see its description)

PA5415 is regulated by 79 influences and regulates 0 modules.
Regulators for PA5415 glyA1 (79)
Regulator Module Operator
PA0034 137 tf
PA0248 137 tf
PA0289 137 tf
PA0294 137 tf
PA0367 137 tf
PA0479 137 tf
PA0512 137 tf
PA0675 137 tf
PA0893 137 tf
PA1201 137 tf
PA1261 137 tf
PA1269 137 tf
PA1430 137 tf
PA1633 137 tf
PA1713 137 tf
PA1759 137 tf
PA1760 137 tf
PA1776 137 tf
PA1850 137 tf
PA1853 137 tf
PA1949 137 tf
PA1998 137 tf
PA2010 137 tf
PA2016 137 tf
PA2020 137 tf
PA2246 137 tf
PA2320 137 tf
PA2469 137 tf
PA2484 137 tf
PA2591 137 tf
PA2849 137 tf
PA3002 137 tf
PA3126 137 tf
PA3965 137 tf
PA4070 137 tf
PA4182 137 tf
PA4185 137 tf
PA4269 137 tf
PA4451 137 tf
PA4787 137 tf
PA5157 137 tf
PA5253 137 tf
PA5274 137 tf
PA5324 137 tf
PA5380 137 tf
PA0121 146 tf
PA0207 146 tf
PA0294 146 tf
PA0512 146 tf
PA0708 146 tf
PA0893 146 tf
PA1015 146 tf
PA1099 146 tf
PA1309 146 tf
PA1430 146 tf
PA1633 146 tf
PA1713 146 tf
PA1760 146 tf
PA1853 146 tf
PA1859 146 tf
PA1949 146 tf
PA1998 146 tf
PA2010 146 tf
PA2016 146 tf
PA2020 146 tf
PA2115 146 tf
PA2121 146 tf
PA2320 146 tf
PA2484 146 tf
PA2511 146 tf
PA3363 146 tf
PA3565 146 tf
PA4070 146 tf
PA4132 146 tf
PA4196 146 tf
PA4275 146 tf
PA4769 146 tf
PA4787 146 tf
PA5085 146 tf

Warning: PA5415 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
3104 4.40e+02 aCgataAcAAcaAgGa
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3105 1.30e+03 CtCCCCGTgGC
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3122 2.60e+02 TtgTTGAA
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3123 6.90e+03 TGGAAAAACA
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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 PA5415

PA5415 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 PA5415

PA5415 has total of 24 gene neighbors in modules 137, 146
Gene neighbors (24)
Gene Common Name Description Module membership
PA0049 PA0049 hypothetical protein (NCBI) 146, 365
PA0865 hpd 4-hydroxyphenylpyruvate dioxygenase (NCBI) 137, 146
PA0870 phhC aromatic amino acid aminotransferase (NCBI) 137, 430
PA0871 phhB pterin-4-alpha-carbinolamine dehydratase (NCBI) 137, 430
PA0872 phhA phenylalanine-4-hydroxylase (NCBI) 137, 430
PA1999 PA1999 probable CoA transferase, subunit A (NCBI) 146, 502
PA2000 PA2000 probable CoA transferase, subunit B (NCBI) 146, 502
PA2001 atoB acetyl-CoA acetyltransferase (NCBI) 146, 365
PA2007 maiA maleylacetoacetate isomerase (NCBI) 137, 365
PA2008 fahA fumarylacetoacetase (NCBI) 137, 146
PA2009 hmgA homogentisate 1,2-dioxygenase (NCBI) 137, 146
PA2109 PA2109 hypothetical protein (NCBI) 146, 365
PA2110 PA2110 hypothetical protein (NCBI) 146, 365
PA2111 PA2111 hypothetical protein (NCBI) 146, 365
PA2112 PA2112 hypothetical protein (NCBI) 146, 365
PA2113 PA2113 probable porin (NCBI) 146, 365
PA2114 PA2114 probable major facilitator superfamily (MFS) transporter (NCBI) 146, 365
PA2116 PA2116 hypothetical protein (NCBI) 146, 365
PA2442 gcvT2 glycine cleavage system protein T2 (NCBI) 137, 146
PA2443 sdaA L-serine dehydratase (NCBI) 137, 146
PA2444 glyA2 serine hydroxymethyltransferase (NCBI) 137, 146
PA2445 gcvP2 glycine cleavage system protein P2 (NCBI) 137, 146
PA2446 gcvH2 glycine cleavage system protein H2 (NCBI) 137, 146
PA5415 glyA1 serine hydroxymethyltransferase (NCBI) 137, 146
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 PA5415
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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