Organism : Pseudomonas aeruginosa | Module List :
PA2588

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2588
(Mouseover regulator name to see its description)

PA2588 is regulated by 15 influences and regulates 33 modules.
Regulators for PA2588 (15)
Regulator Module Operator
PA1003 164 tf
PA2588 164 tf
PA2591 164 tf
PA2718 164 tf
PA4778 164 tf
PA1663 112 tf
PA2332 112 tf
PA2588 112 tf
PA2591 112 tf
PA3477 112 tf
PA4132 112 tf
PA4703 112 tf
PA5059 112 tf
PA5274 112 tf
PA5562 112 tf

Warning: PA2588 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
3056 2.40e-04 aaCtaccagttcTggcAGgt
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3057 8.40e-02 ATGcgTttgaagtTt
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3156 2.30e-08 aaGAagacatcCAatttgCATAAt
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3157 7.60e-07 AcCTAtCtgAacTGcTagttatga
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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 PA2588

PA2588 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for PA2588

PA2588 has total of 41 gene neighbors in modules 112, 164
Gene neighbors (41)
Gene Common Name Description Module membership
PA0122 PA0122 hypothetical protein (NCBI) 112, 124
PA0852 cbpD chitin-binding protein CbpD precursor (NCBI) 112, 124
PA0996 pqsA probable coenzyme A ligase (NCBI) 17, 164
PA0997 pqsB beta-keto-acyl-acyl-carrier protein synthase-like protein (NCBI) 17, 164
PA0998 pqsC beta-keto-acyl-acyl-carrier protein synthase-like protein (NCBI) 17, 164
PA0999 pqsD 3-oxoacyl-[acyl-carrier-protein] synthase III (NCBI) 17, 164
PA1000 pqsE Quinolone signal response protein (NCBI) 17, 164
PA1001 phnA anthranilate synthase component I (NCBI) 17, 164
PA1002 phnB anthranilate synthase component II (NCBI) 17, 164
PA1003 mvfR Transcriptional regulator (NCBI) 17, 164
PA1130 rhlC rhamnosyltransferase 2 (NCBI) 112, 472
PA1131 PA1131 probable major facilitator superfamily (MFS) transporter (NCBI) 112, 472
PA1245 PA1245 hypothetical protein (NCBI) 127, 164
PA1250 aprI alkaline proteinase inhibitor AprI (NCBI) 112, 164
PA1431 rsaL regulatory protein RsaL (NCBI) 17, 164
PA1432 lasI autoinducer synthesis protein LasI (NCBI) 17, 164
PA1869 PA1869 probable acyl carrier protein (NCBI) 112, 124
PA2587 pqsH probable FAD-dependent monooxygenase (NCBI) 17, 164
PA2588 PA2588 probable transcriptional regulator (NCBI) 112, 164
PA2591 PA2591 probable transcriptional regulator (NCBI) 112, 164
PA2592 PA2592 probable periplasmic spermidine/putrescine-binding protein (NCBI) 112, 164
PA3326 PA3326 probable Clp-family ATP-dependent protease (NCBI) 112, 124
PA3361 lecB fucose-binding lectin PA-IIL (NCBI) 112, 124
PA3476 rhlI autoinducer synthesis protein RhlI (NCBI) 112, 164
PA3477 rhlR transcriptional regulator RhlR (NCBI) 112, 402
PA3478 rhlB rhamnosyltransferase chain B (NCBI) 112, 124
PA3479 rhlA rhamnosyltransferase chain A (NCBI) 112, 124
PA3520 PA3520 hypothetical protein (NCBI) 112, 124
PA3724 lasB elastase LasB (NCBI) 112, 124
PA3904 PA3904 hypothetical protein (NCBI) 17, 164
PA3905 PA3905 hypothetical protein (NCBI) 17, 164
PA3906 PA3906 hypothetical protein (NCBI) 17, 164
PA3907 PA3907 hypothetical protein (NCBI) 17, 164
PA3908 PA3908 hypothetical protein (NCBI) 17, 164
PA4141 PA4141 hypothetical protein (NCBI) 112, 124
PA4142 PA4142 probable secretion protein (NCBI) 112, 473
PA4143 PA4143 probable toxin transporter (NCBI) 112, 473
PA4144 PA4144 probable outer membrane protein precursor (NCBI) 112, 473
PA4190 pqsL probable FAD-dependent monooxygenase (NCBI) 35, 164
PA4209 phzM probable phenazine-specific methyltransferase (NCBI) 112, 250
PA5219 PA5219 hypothetical protein (NCBI) 112, 472
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 PA2588
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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