Organism : Pseudomonas aeruginosa | Module List :
PA2516 xylZ

toluate 1,2-dioxygenase electron transfer component (NCBI)

CircVis
Functional Annotations (10)
Function System
Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrF cog/ cog
electron transport go/ biological_process
electron carrier activity go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
2 iron, 2 sulfur cluster binding go/ molecular_function
Benzoate degradation kegg/ kegg pathway
Fluorobenzoate degradation kegg/ kegg pathway
Xylene degradation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2516
(Mouseover regulator name to see its description)

PA2516 is regulated by 36 influences and regulates 0 modules.
Regulators for PA2516 xylZ (36)
Regulator Module Operator
PA1109 172 tf
PA1351 172 tf
PA1603 172 tf
PA1980 172 tf
PA2519 172 tf
PA2737 172 tf
PA2838 172 tf
PA3045 172 tf
PA3249 172 tf
PA3381 172 tf
PA3420 172 tf
PA3596 172 tf
PA3711 172 tf
PA3771 172 tf
PA5032 172 tf
PA0191 285 tf
PA0512 285 tf
PA0701 285 tf
PA0748 285 tf
PA1347 285 tf
PA1949 285 tf
PA1980 285 tf
PA2258 285 tf
PA2276 285 tf
PA2354 285 tf
PA2547 285 tf
PA2838 285 tf
PA3045 285 tf
PA3381 285 tf
PA3420 285 tf
PA3596 285 tf
PA3630 285 tf
PA3711 285 tf
PA4341 285 tf
PA4989 285 tf
PA5562 285 tf

Warning: PA2516 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
3172 3.00e-02 AaaaA.AacgaAgcc
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3173 6.00e+00 AAaacaTCGcgAaGAagaCaa
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3398 1.50e-03 aAcaAcaaCAA
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3399 1.10e+04 tATttCcgTtG
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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 PA2516

PA2516 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrF cog/ cog
electron transport go/ biological_process
electron carrier activity go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
2 iron, 2 sulfur cluster binding go/ molecular_function
Benzoate degradation kegg/ kegg pathway
Fluorobenzoate degradation kegg/ kegg pathway
Xylene degradation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Module neighborhood information for PA2516

PA2516 has total of 34 gene neighbors in modules 172, 285
Gene neighbors (34)
Gene Common Name Description Module membership
PA0321 PA0321 probable acetylpolyamine aminohydrolase (NCBI) 172, 310
PA0439 PA0439 dihydropyrimidine dehydrogenase (NCBI) 285, 481
PA0440 PA0440 probable oxidoreductase (NCBI) 285, 481
PA0480 PA0480 probable hydrolase (NCBI) 172, 285
PA0843 plcR phospholipase accessory protein PlcR precursor (NCBI) 172, 328
PA0844 plcH hemolytic phospholipase C precursor (NCBI) 172, 310
PA1108 PA1108 probable major facilitator superfamily (MFS) transporter (NCBI) 172, 310
PA1109 PA1109 probable transcriptional regulator (NCBI) 172, 311
PA1972 PA1972 hypothetical protein (NCBI) 12, 172
PA2133 PA2133 hypothetical protein (NCBI) 36, 285
PA2214 PA2214 probable major facilitator superfamily (MFS) transporter (NCBI) 148, 285
PA2215 PA2215 hypothetical protein (NCBI) 285, 428
PA2348 PA2348 hypothetical protein (NCBI) 285, 304
PA2472 PA2472 probable major facilitator superfamily (MFS) transporter (NCBI) 285, 304
PA2474 PA2474 hypothetical protein (NCBI) 285, 304
PA2509 catB muconate cycloisomerase I (NCBI) 172, 500
PA2515 xylL cis-1,2-dihydroxycyclohexa-3,4-diene carboxylate dehydrogenase (NCBI) 104, 172
PA2516 xylZ toluate 1,2-dioxygenase electron transfer component (NCBI) 172, 285
PA2517 xylY toluate 1,2-dioxygenase beta subunit (NCBI) 172, 285
PA2518 xylX toluate 1,2-dioxygenase alpha subunit (NCBI) 172, 285
PA2519 xylS transcriptional regulator XylS (NCBI) 172, 446
PA2924 hisQ histidine transport system permease HisQ (NCBI) 36, 285
PA2926 hisP histidine transport protein HisP (NCBI) 92, 285
PA3249 PA3249 probable transcriptional regulator (NCBI) 172, 450
PA3467 PA3467 probable major facilitator superfamily (MFS) transporter (NCBI) 172, 310
PA4071 PA4071 hypothetical protein (NCBI) 36, 285
PA4072 PA4072 probable amino acid permease (NCBI) 36, 285
PA4085 cupB2 chaperone CupB2 (NCBI) 158, 285
PA4087 PA4087 hypothetical protein (NCBI) 235, 285
PA4088 PA4088 probable aminotransferase (NCBI) 36, 285
PA4089 PA4089 probable short-chain dehydrogenase (NCBI) 36, 285
PA4100 PA4100 probable dehydrogenase (NCBI) 125, 285
PA4343 PA4343 probable major facilitator superfamily (MFS) transporter (NCBI) 12, 172
PA4540 PA4540 hypothetical protein (NCBI) 172, 310
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 PA2516
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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