Organism : Pseudomonas aeruginosa | Module List :
PA3594

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3594
(Mouseover regulator name to see its description)

PA3594 is regulated by 28 influences and regulates 36 modules.
Regulators for PA3594 (28)
Regulator Module Operator
PA0207 355 tf
PA0707 355 tf
PA1351 355 tf
PA1467 355 tf
PA1599 355 tf
PA2016 355 tf
PA2848 355 tf
PA3067 355 tf
PA3594 355 tf
PA3778 355 tf
PA0056 463 tf
PA0133 463 tf
PA0306 463 tf
PA0701 463 tf
PA0828 463 tf
PA1109 463 tf
PA1351 463 tf
PA1399 463 tf
PA1826 463 tf
PA2050 463 tf
PA2376 463 tf
PA3002 463 tf
PA3045 463 tf
PA3381 463 tf
PA3594 463 tf
PA3714 463 tf
PA3771 463 tf
PA5032 463 tf

Warning: PA3594 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
3534 3.20e+01 TTTTcctAtgtaaGgcgcTgA
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3535 7.00e+01 gGccaGgtggcGGA
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3742 5.00e-09 atAAGaAAaACA
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3743 2.20e-08 CgcGGcGaatcCttCGAaAA.C
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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 PA3594

PA3594 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for PA3594

PA3594 has total of 43 gene neighbors in modules 355, 463
Gene neighbors (43)
Gene Common Name Description Module membership
PA0204 PA0204 probable permease of ABC transporter (NCBI) 324, 355
PA0205 PA0205 probable permease of ABC transporter (NCBI) 324, 355
PA0206 PA0206 probable ATP-binding component of ABC transporter (NCBI) 355, 362
PA0207 PA0207 probable transcriptional regulator (NCBI) 355, 366
PA0241 PA0241 probable major facilitator superfamily (MFS) transporter (NCBI) 25, 463
PA0344 PA0344 hypothetical protein (NCBI) 163, 355
PA0345 PA0345 hypothetical protein (NCBI) 246, 355
PA0346 PA0346 hypothetical protein (NCBI) 109, 355
PA0368 PA0368 hypothetical protein (NCBI) 320, 355
PA0434 PA0434 hypothetical protein (NCBI) 355, 516
PA0707 toxR transcriptional regulator ToxR (NCBI) 119, 355
PA0818 PA0818 hypothetical protein (NCBI) 355, 516
PA1146 PA1146 probable iron-containing alcohol dehydrogenase (NCBI) 359, 463
PA1148 toxA exotoxin A precursor (NCBI) 156, 355
PA1149 PA1149 hypothetical protein (NCBI) 62, 355
PA1154 PA1154 hypothetical protein (NCBI) 156, 355
PA1405 PA1405 probable helicase (NCBI) 190, 355
PA1826 PA1826 probable transcriptional regulator (NCBI) 373, 463
PA1827 PA1827 probable short-chain dehydrogenase (NCBI) 366, 463
PA2694 PA2694 probable thioredoxin (NCBI) 187, 355
PA2783 PA2783 hypothetical protein (NCBI) 190, 355
PA2848 PA2848 probable transcriptional regulator (NCBI) 355, 537
PA2909 PA2909 precorrin-6x reductase (NCBI) 49, 355
PA3219 PA3219 hypothetical protein (NCBI) 211, 463
PA3424 PA3424 hypothetical protein (NCBI) 355, 483
PA3589 PA3589 acetyl-CoA acetyltransferase (NCBI) 36, 463
PA3590 PA3590 probable hydroxyacyl-CoA dehydrogenase (NCBI) 333, 463
PA3591 PA3591 probable enoyl-CoA hydratase/isomerase (NCBI) 36, 463
PA3592 PA3592 hypothetical protein (NCBI) 394, 463
PA3593 PA3593 probable acyl-CoA dehydrogenase (NCBI) 359, 463
PA3594 PA3594 probable transcriptional regulator (NCBI) 355, 463
PA4018 PA4018 hypothetical protein (NCBI) 320, 355
PA4364 PA4364 hypothetical protein (NCBI) 463, 534
PA4365 PA4365 probable transporter (NCBI) 109, 463
PA4816 PA4816 hypothetical protein (NCBI) 355, 486
PA4818 PA4818 hypothetical protein (NCBI) 180, 463
PA4819 PA4819 probable glycosyl transferase (NCBI) 180, 463
PA4820 PA4820 hypothetical protein (NCBI) 311, 463
PA4821 PA4821 probable transporter (NCBI) 335, 463
PA4887 PA4887 probable major facilitator superfamily (MFS) transporter (NCBI) 355, 377
PA5385 PA5385 hypothetical protein (NCBI) 177, 463
PA5477 PA5477 hypothetical protein (NCBI) 321, 355
PA5517 PA5517 hypothetical protein (NCBI) 355, 377
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 PA3594
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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