Organism : Pseudomonas aeruginosa | Module List :
PA3006 psrA

transcriptional regulator PsrA (NCBI)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3006
(Mouseover regulator name to see its description)

PA3006 is regulated by 25 influences and regulates 26 modules.
Regulators for PA3006 psrA (25)
Regulator Module Operator
PA0424 460 tf
PA0610 460 tf
PA0762 460 tf
PA0831 460 tf
PA1241 460 tf
PA1300 460 tf
PA1467 460 tf
PA2277 460 tf
PA2337 460 tf
PA2825 460 tf
PA3006 460 tf
PA3007 460 tf
PA3815 460 tf
PA4745 460 tf
PA5438 460 tf
PA0610 468 tf
PA0611 468 tf
PA0831 468 tf
PA0906 468 tf
PA1300 468 tf
PA1335 468 tf
PA3006 468 tf
PA3007 468 tf
PA4984 468 tf
PA5365 468 tf

Warning: PA3006 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
3736 2.40e-08 ttTgaCTGt.tAttcaTACAGTaa
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3737 1.20e+00 Aaa.Act.ggCaacTTcAtcGtGA
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3752 6.60e-19 attActgTATg.aaataCAgttAt
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3753 7.60e-06 AcAgAaatgaCacGgaaAaCggAt
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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 PA3006

PA3006 is enriched for 5 functions in 3 categories.
Module neighborhood information for PA3006

PA3006 has total of 33 gene neighbors in modules 460, 468
Gene neighbors (33)
Gene Common Name Description Module membership
PA0424 mexR multidrug resistance operon repressor MexR (NCBI) 224, 460
PA0610 prtN transcriptional regulator PrtN (NCBI) 11, 468
PA0611 prtR transcriptional regulator PrtR (NCBI) 11, 468
PA0613 PA0613 hypothetical protein (NCBI) 11, 468
PA0670 PA0670 hypothetical protein (NCBI) 468, 542
PA0671 PA0671 hypothetical protein (NCBI) 468, 542
PA0805 PA0805 hypothetical protein (NCBI) 251, 460
PA0906 PA0906 probable transcriptional regulator (NCBI) 11, 468
PA0907 PA0907 hypothetical protein (NCBI) 243, 468
PA0913 mgtE probable Mg transporter MgtE (NCBI) 412, 460
PA0922 PA0922 hypothetical protein (NCBI) 460, 468
PA1029 PA1029 hypothetical protein (NCBI) 376, 460
PA1030 PA1030 hypothetical protein (NCBI) 376, 460
PA1296 PA1296 probable 2-hydroxyacid dehydrogenase (NCBI) 251, 460
PA2288 PA2288 hypothetical protein (NCBI) 460, 468
PA3006 psrA transcriptional regulator PsrA (NCBI) 460, 468
PA3007 lexA LexA repressor (NCBI) 460, 468
PA3008 PA3008 hypothetical protein (NCBI) 460, 468
PA3413 PA3413 hypothetical protein (NCBI) 460, 468
PA3414 PA3414 hypothetical protein (NCBI) 460, 468
PA3616 recX RecA regulator RecX (NCBI) 460, 468
PA3617 recA recombinase A (NCBI) 460, 468
PA3730 PA3730 hypothetical protein (NCBI) 212, 468
PA3731 PA3731 hypothetical protein (NCBI) 376, 468
PA3732 PA3732 hypothetical protein (NCBI) 376, 468
PA4763 recN DNA repair protein RecN (NCBI) 460, 468
PA4826 PA4826 hypothetical protein (NCBI) 412, 460
PA5470 PA5470 peptide chain release factor 2 (NCBI) 412, 460
PA5471 PA5471 hypothetical protein (NCBI) 412, 460
PA5522 PA5522 probable glutamine synthetase (NCBI) 243, 468
PA5523 PA5523 probable aminotransferase (NCBI) 243, 468
PA5524 PA5524 probable short-chain dehydrogenase (NCBI) 243, 468
PA5525 PA5525 probable transcriptional regulator (NCBI) 243, 468
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 PA3006
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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