Organism : Pseudomonas aeruginosa | Module List :
PA3328

probable FAD-dependent monooxygenase (NCBI)

CircVis
Functional Annotations (4)
Function System
2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases cog/ cog
monooxygenase activity go/ molecular_function
electron transport go/ biological_process
cellular aromatic compound metabolic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3328
(Mouseover regulator name to see its description)

PA3328 is regulated by 50 influences and regulates 0 modules.
Regulators for PA3328 (50)
Regulator Module Operator
PA0367 447 tf
PA0784 447 tf
PA0876 447 tf
PA1226 447 tf
PA1241 447 tf
PA1619 447 tf
PA1663 447 tf
PA1776 447 tf
PA2277 447 tf
PA2299 447 tf
PA2320 447 tf
PA2468 447 tf
PA2484 447 tf
PA2497 447 tf
PA2510 447 tf
PA2591 447 tf
PA3006 447 tf
PA3477 447 tf
PA3587 447 tf
PA3699 447 tf
PA4132 447 tf
PA4288 447 tf
PA4784 447 tf
PA5116 447 tf
PA5356 447 tf
PA5428 447 tf
PA0367 527 tf
PA0784 527 tf
PA0876 527 tf
PA1226 527 tf
PA1241 527 tf
PA1619 527 tf
PA1663 527 tf
PA2277 527 tf
PA2299 527 tf
PA2320 527 tf
PA2468 527 tf
PA2484 527 tf
PA2510 527 tf
PA2591 527 tf
PA3006 527 tf
PA3126 527 tf
PA3477 527 tf
PA3699 527 tf
PA3973 527 tf
PA4132 527 tf
PA5116 527 tf
PA5356 527 tf
PA5403 527 tf
PA5428 527 tf

Warning: PA3328 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
3714 8.70e+02 TCgcCtTCga.cAtcCAtC
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3715 3.50e+03 AGCTGGAA
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3868 8.70e+02 TCgcCtTCga.cAtcCAtC
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3869 3.50e+03 AGCTGGAA
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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 PA3328

PA3328 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases cog/ cog
monooxygenase activity go/ molecular_function
electron transport go/ biological_process
cellular aromatic compound metabolic process go/ biological_process
Module neighborhood information for PA3328

PA3328 has total of 10 gene neighbors in modules 447, 527
Gene neighbors (10)
Gene Common Name Description Module membership
PA3327 PA3327 probable non-ribosomal peptide synthetase (NCBI) 447, 527
PA3328 PA3328 probable FAD-dependent monooxygenase (NCBI) 447, 527
PA3329 PA3329 hypothetical protein (NCBI) 447, 527
PA3330 PA3330 probable short chain dehydrogenase (NCBI) 447, 527
PA3331 PA3331 cytochrome P450 (NCBI) 447, 527
PA3332 PA3332 hypothetical protein (NCBI) 447, 527
PA3333 fabH2 3-oxoacyl-[acyl-carrier-protein] synthase III (NCBI) 447, 527
PA3334 PA3334 probable acyl carrier protein (NCBI) 447, 527
PA3335 PA3335 hypothetical protein (NCBI) 447, 527
PA3336 PA3336 probable major facilitator superfamily (MFS) transporter (NCBI) 447, 527
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 PA3328
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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