Organism : Pseudomonas aeruginosa | Module List :
PA4003 pbpA

penicillin-binding protein 2 (NCBI)

CircVis
Functional Annotations (5)
Function System
Cell division protein FtsI/penicillin-binding protein 2 cog/ cog
penicillin binding go/ molecular_function
peptidoglycan-based cell wall biogenesis go/ biological_process
Peptidoglycan biosynthesis kegg/ kegg pathway
pbp2_mrdA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4003
(Mouseover regulator name to see its description)

PA4003 is regulated by 45 influences and regulates 0 modules.
Regulators for PA4003 pbpA (45)
Regulator Module Operator
PA0393 552 tf
PA0611 552 tf
PA0765 552 tf
PA0893 552 tf
PA0905 552 tf
PA1526 552 tf
PA2586 552 tf
PA2622 552 tf
PA2849 552 tf
PA3002 552 tf
PA3067 552 tf
PA3124 552 tf
PA3565 552 tf
PA3583 552 tf
PA3804 552 tf
PA4070 552 tf
PA4074 552 tf
PA4185 552 tf
PA4238 552 tf
PA4269 552 tf
PA4462 552 tf
PA4755 552 tf
PA4787 552 tf
PA5166 552 tf
PA5239 552 tf
PA5301 552 tf
PA5550 552 tf
PA5562 552 tf
PA0893 204 tf
PA0961 204 tf
PA1504 204 tf
PA1898 204 tf
PA2622 204 tf
PA2696 204 tf
PA3002 204 tf
PA3804 204 tf
PA4052 204 tf
PA4269 204 tf
PA4270 204 tf
PA4853 204 tf
PA4890 204 tf
PA5261 204 tf
PA5511 204 tf
PA5550 204 tf
PA5562 204 tf

Warning: PA4003 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
3236 4.50e+00 AcAAtcGcgccTTTCcccta
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3237 3.20e+02 TGGcgAAaTA
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3916 1.60e-05 CcCgttAtAatCccgcatTt
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3917 2.90e+00 AaAACGGatGgGTAtCctAGCAT
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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 PA4003

PA4003 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Cell division protein FtsI/penicillin-binding protein 2 cog/ cog
penicillin binding go/ molecular_function
peptidoglycan-based cell wall biogenesis go/ biological_process
Peptidoglycan biosynthesis kegg/ kegg pathway
pbp2_mrdA tigr/ tigrfam
Module neighborhood information for PA4003

PA4003 has total of 30 gene neighbors in modules 204, 552
Gene neighbors (30)
Gene Common Name Description Module membership
PA0169 PA0169 hypothetical protein (NCBI) 204, 363
PA0170 PA0170 hypothetical protein (NCBI) 204, 363
PA0171 PA0171 hypothetical protein (NCBI) 204, 363
PA0172 PA0172 hypothetical protein (NCBI) 204, 363
PA0369 PA0369 hypothetical protein (NCBI) 37, 552
PA0371 PA0371 hypothetical protein (NCBI) 37, 552
PA0372 PA0372 probable zinc protease (NCBI) 341, 552
PA0373 ftsY signal recognition particle receptor FtsY (NCBI) 424, 552
PA0374 ftsE cell division protein FtsE (NCBI) 18, 552
PA0768 lepB signal peptidase I (NCBI) 204, 426
PA2992 PA2992 hypothetical protein (NCBI) 43, 552
PA3640 dnaE DNA polymerase III subunit alpha (NCBI) 270, 552
PA3763 purL phosphoribosylformylglycinamidine synthase (NCBI) 106, 204
PA3769 guaA bifunctional GMP synthase/glutamine amidotransferase protein (NCBI) 43, 204
PA4003 pbpA penicillin-binding protein 2 (NCBI) 204, 552
PA4458 PA4458 hypothetical protein (NCBI) 262, 552
PA4459 PA4459 hypothetical protein (NCBI) 262, 552
PA4664 hemK probable methyl transferase (NCBI) 204, 426
PA4686 PA4686 hypothetical protein (NCBI) 204, 350
PA4856 retS regulator of exopolysaccharide and type III secretion (NCBI) 59, 552
PA5004 PA5004 probable glycosyl transferase (NCBI) 204, 426
PA5006 PA5006 hypothetical protein (NCBI) 204, 421
PA5007 PA5007 hypothetical protein (NCBI) 204, 421
PA5010 waaG UDP-glucose:(heptosyl) LPS alpha 1,3-glucosyltransferase WaaG (NCBI) 204, 421
PA5011 waaC heptosyltransferase I (NCBI) 204, 421
PA5012 waaF heptosyltransferase II (NCBI) 98, 204
PA5070 tatC transport protein TatC (NCBI) 75, 552
PA5077 mdoH glucosyltransferase MdoH (NCBI) 91, 552
PA5140 hisF1 imidazole glycerol phosphate synthase subunit HisF (NCBI) 204, 353
PA5141 hisA 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase (NCBI) 204, 260
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 PA4003
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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