Organism : Pseudomonas aeruginosa | Module List :
PA2129 cupA2

chaperone CupA2 (NCBI)

CircVis
Functional Annotations (4)
Function System
P pilus assembly protein, chaperone PapD cog/ cog
protein binding go/ molecular_function
cellular cell wall organization go/ biological_process
outer membrane-bounded periplasmic space go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2129
(Mouseover regulator name to see its description)

PA2129 is regulated by 49 influences and regulates 0 modules.
Regulators for PA2129 cupA2 (49)
Regulator Module Operator
PA0056 36 tf
PA0191 36 tf
PA0306 36 tf
PA0393 36 tf
PA0512 36 tf
PA0701 36 tf
PA0748 36 tf
PA0784 36 tf
PA0893 36 tf
PA1285 36 tf
PA1347 36 tf
PA1351 36 tf
PA1949 36 tf
PA1980 36 tf
PA2276 36 tf
PA2547 36 tf
PA3045 36 tf
PA3249 36 tf
PA3381 36 tf
PA3420 36 tf
PA3596 36 tf
PA3711 36 tf
PA3771 36 tf
PA3932 36 tf
PA4074 36 tf
PA4341 36 tf
PA5032 36 tf
PA5293 36 tf
PA5382 36 tf
PA5562 36 tf
PA0306 439 tf
PA0701 439 tf
PA0828 439 tf
PA0893 439 tf
PA1347 439 tf
PA1374 439 tf
PA1399 439 tf
PA1980 439 tf
PA2510 439 tf
PA2681 439 tf
PA2696 439 tf
PA2838 439 tf
PA3381 439 tf
PA3420 439 tf
PA3594 439 tf
PA3714 439 tf
PA3778 439 tf
PA4057 439 tf
PA4174 439 tf

Warning: PA2129 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
2904 8.20e-02 aAcaAcaAC.aat..AAgaat
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2905 6.50e+03 AcaTCatcaA.cAgt
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3698 2.30e+03 AAGAAGGAA
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3699 6.10e+03 GaTgatC.gaTtGgt
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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 PA2129

PA2129 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
P pilus assembly protein, chaperone PapD cog/ cog
protein binding go/ molecular_function
cellular cell wall organization go/ biological_process
outer membrane-bounded periplasmic space go/ cellular_component
Module neighborhood information for PA2129

PA2129 has total of 36 gene neighbors in modules 36, 439
Gene neighbors (36)
Gene Common Name Description Module membership
PA0057 PA0057 hypothetical protein (NCBI) 333, 439
PA0189 PA0189 probable porin (NCBI) 36, 201
PA0453 PA0453 hypothetical protein (NCBI) 434, 439
PA1025 PA1025 probable porin (NCBI) 36, 425
PA1187 PA1187 probable acyl-CoA dehydrogenase (NCBI) 366, 439
PA1253 PA1253 probable semialdehyde dehydrogenase (NCBI) 201, 439
PA1267 PA1267 hypothetical protein (NCBI) 16, 36
PA1346 PA1346 hypothetical protein (NCBI) 36, 158
PA1916 PA1916 probable amino acid permease (NCBI) 439, 534
PA1917 PA1917 hypothetical protein (NCBI) 394, 439
PA1918 PA1918 hypothetical protein (NCBI) 201, 439
PA2124 PA2124 probable dehydrogenase (NCBI) 12, 36
PA2129 cupA2 chaperone CupA2 (NCBI) 36, 439
PA2130 cupA3 usher CupA3 (NCBI) 439, 471
PA2131 cupA4 fimbrial subunit CupA4 (NCBI) 439, 471
PA2132 cupA5 chaperone CupA5 (NCBI) 439, 471
PA2133 PA2133 hypothetical protein (NCBI) 36, 285
PA2216 PA2216 hypothetical protein (NCBI) 289, 439
PA2217 PA2217 probable aldehyde dehydrogenase (NCBI) 36, 340
PA2924 hisQ histidine transport system permease HisQ (NCBI) 36, 285
PA3279 oprP Phosphate-specific outer membrane porin OprP precursor (NCBI) 132, 439
PA3395 nosY NosY protein (NCBI) 36, 497
PA3589 PA3589 acetyl-CoA acetyltransferase (NCBI) 36, 463
PA3591 PA3591 probable enoyl-CoA hydratase/isomerase (NCBI) 36, 463
PA3774 PA3774 probable acetylpolyamine aminohydrolase (NCBI) 439, 486
PA4071 PA4071 hypothetical protein (NCBI) 36, 285
PA4072 PA4072 probable amino acid permease (NCBI) 36, 285
PA4083 cupB4 chaperone CupB4 (NCBI) 36, 439
PA4084 cupB3 usher CupB3 (NCBI) 12, 36
PA4088 PA4088 probable aminotransferase (NCBI) 36, 285
PA4089 PA4089 probable short-chain dehydrogenase (NCBI) 36, 285
PA4137 PA4137 probable porin (NCBI) 36, 177
PA4166 PA4166 probable acetyltransferase (NCBI) 439, 459
PA4814 fadH2 2,4-dienoyl-CoA reductase FadH2 (NCBI) 180, 439
PA4884 PA4884 hypothetical protein (NCBI) 418, 439
PA5090 PA5090 hypothetical protein (NCBI) 439, 473
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 PA2129
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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