Organism : Pseudomonas aeruginosa | Module List :
PA3438 folE1

GTP cyclohydrolase I precursor (NCBI)

CircVis
Functional Annotations (7)
Function System
GTP cyclohydrolase I cog/ cog
GTP cyclohydrolase I activity go/ molecular_function
cytoplasm go/ cellular_component
aromatic compound biosynthetic process go/ biological_process
Folate biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
folE tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3438
(Mouseover regulator name to see its description)

PA3438 is regulated by 37 influences and regulates 0 modules.
Regulators for PA3438 folE1 (37)
Regulator Module Operator
PA0393 511 tf
PA0455 511 tf
PA0890 511 tf
PA0893 511 tf
PA3002 511 tf
PA3321 511 tf
PA3563 511 tf
PA3804 511 tf
PA4145 511 tf
PA4530 511 tf
PA5274 511 tf
PA5562 511 tf
PA0125 380 tf
PA0167 380 tf
PA0393 380 tf
PA0890 380 tf
PA0893 380 tf
PA1300 380 tf
PA1335 380 tf
PA1397 380 tf
PA1430 380 tf
PA1760 380 tf
PA1859 380 tf
PA1945 380 tf
PA1980 380 tf
PA2577 380 tf
PA2588 380 tf
PA2591 380 tf
PA2917 380 tf
PA3002 380 tf
PA3699 380 tf
PA3714 380 tf
PA3804 380 tf
PA4270 380 tf
PA4493 380 tf
PA5253 380 tf
PA5403 380 tf

Warning: PA3438 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
3584 1.70e-01 CgcTggaaatcTttgaccgaTccc
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3585 4.00e+03 tTtcggaAatgCgacaggAA
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3836 9.60e-01 t.C..gcCTTGcC.GCgCaG.Ca
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3837 3.20e+01 AAAGCgTTtCGCTACtGCCggCCC
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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 PA3438

PA3438 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
GTP cyclohydrolase I cog/ cog
GTP cyclohydrolase I activity go/ molecular_function
cytoplasm go/ cellular_component
aromatic compound biosynthetic process go/ biological_process
Folate biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
folE tigr/ tigrfam
Module neighborhood information for PA3438

PA3438 has total of 53 gene neighbors in modules 380, 511
Gene neighbors (53)
Gene Common Name Description Module membership
PA0305 PA0305 hypothetical protein (NCBI) 375, 380
PA0361 PA0361 probable gamma-glutamyltranspeptidase precursor (NCBI) 306, 511
PA0895 aruC N-succinylglutamate 5-semialdehyde dehydrogenase (NCBI) 122, 380
PA0896 aruF arginine/ornithine succinyltransferase AI subunit (NCBI) 191, 380
PA0897 aruG arginine/ornithine succinyltransferase AII subunit (NCBI) 191, 380
PA0898 aruD succinylglutamate 5-semialdehyde dehydrogenase (NCBI) 191, 380
PA0899 aruB succinylarginine dihydrolase (NCBI) 191, 380
PA1005 PA1005 hypothetical protein (NCBI) 361, 380
PA1060 PA1060 hypothetical protein (NCBI) 321, 511
PA1061 PA1061 hypothetical protein (NCBI) 203, 511
PA1062 PA1062 hypothetical protein (NCBI) 203, 511
PA1530 PA1530 hypothetical protein (NCBI) 91, 511
PA1548 PA1548 hypothetical protein (NCBI) 46, 511
PA1549 PA1549 probable cation-transporting P-type ATPase (NCBI) 46, 511
PA1683 PA1683 hypothetical protein (NCBI) 214, 511
PA1807 PA1807 probable ATP-binding component of ABC transporter (NCBI) 37, 380
PA1808 PA1808 probable permease of ABC transporter (NCBI) 37, 380
PA1809 PA1809 probable permease of ABC transporter (NCBI) 37, 380
PA1810 PA1810 probable binding protein component of ABC transporter (NCBI) 7, 380
PA1811 PA1811 probable solute-binding protein (NCBI) 49, 380
PA1926 PA1926 hypothetical protein (NCBI) 396, 511
PA2625 PA2625 hypothetical protein (NCBI) 493, 511
PA3003 PA3003 hypothetical protein (NCBI) 389, 511
PA3071 PA3071 hypothetical protein (NCBI) 253, 511
PA3075 PA3075 hypothetical protein (NCBI) 253, 511
PA3437 PA3437 short chain dehydrogenase (NCBI) 263, 511
PA3438 folE1 GTP cyclohydrolase I precursor (NCBI) 380, 511
PA3439 folX d-erythro-7,8-dihydroneopterin triphosphate epimerase (NCBI) 380, 511
PA3693 PA3693 hypothetical protein (NCBI) 380, 511
PA3694 PA3694 hypothetical protein (NCBI) 380, 480
PA3695 PA3695 hypothetical protein (NCBI) 7, 380
PA3696 PA3696 hypothetical protein (NCBI) 7, 380
PA3934 PA3934 hypothetical protein (NCBI) 268, 380
PA4054 ribB bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein (NCBI) 130, 511
PA4145 PA4145 probable transcriptional regulator (NCBI) 60, 511
PA4371 PA4371 hypothetical protein (NCBI) 98, 511
PA4375 PA4375 probable RND efflux transporter (NCBI) 20, 380
PA4404 PA4404 hypothetical protein (NCBI) 249, 511
PA4405 PA4405 hypothetical protein (NCBI) 212, 511
PA4604 PA4604 hypothetical protein (NCBI) 3, 511
PA4605 PA4605 hypothetical protein (NCBI) 234, 511
PA4798 PA4798 hypothetical protein (NCBI) 511, 523
PA4864 ureD urease accessory protein (NCBI) 206, 380
PA4865 ureA urease gamma subunit (NCBI) 380, 540
PA4866 PA4866 hypothetical protein (NCBI) 380, 540
PA4867 ureB urease beta subunit (NCBI) 7, 380
PA4868 ureC urease alpha subunit (NCBI) 7, 380
PA4891 ureE urease accessory protein UreE (NCBI) 240, 380
PA4893 ureG urease accessory protein UreG (NCBI) 337, 380
PA4894 PA4894 hypothetical protein (NCBI) 337, 380
PA4973 thiC thiamine biosynthesis protein ThiC (NCBI) 26, 511
PA5132 PA5132 hypothetical protein (NCBI) 374, 511
PA5317 PA5317 probable binding protein component of ABC dipeptide transporter (NCBI) 4, 380
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 PA3438
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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