Organism : Pseudomonas aeruginosa | Module List :
PA2359

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (7)
Function System
Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2359
(Mouseover regulator name to see its description)

PA2359 is regulated by 75 influences and regulates 12 modules.
Regulators for PA2359 (75)
Regulator Module Operator
PA0133 222 tf
PA0155 222 tf
PA0167 222 tf
PA0191 222 tf
PA0764 222 tf
PA0828 222 tf
PA1097 222 tf
PA1153 222 tf
PA1397 222 tf
PA1504 222 tf
PA1599 222 tf
PA1630 222 tf
PA1826 222 tf
PA1998 222 tf
PA2259 222 tf
PA2312 222 tf
PA2334 222 tf
PA2359 222 tf
PA2423 222 tf
PA2489 222 tf
PA2766 222 tf
PA3583 222 tf
PA3845 222 tf
PA3932 222 tf
PA4185 222 tf
PA4238 222 tf
PA4436 222 tf
PA4508 222 tf
PA4530 222 tf
PA4831 222 tf
PA5255 222 tf
PA5324 222 tf
PA5344 222 tf
PA5365 222 tf
PA5374 222 tf
PA5506 222 tf
PA5525 222 tf
PA0133 406 tf
PA0167 406 tf
PA0191 406 tf
PA0243 406 tf
PA0472 406 tf
PA0764 406 tf
PA0876 406 tf
PA1138 406 tf
PA1504 406 tf
PA1599 406 tf
PA1630 406 tf
PA1859 406 tf
PA1998 406 tf
PA2100 406 tf
PA2123 406 tf
PA2258 406 tf
PA2259 406 tf
PA2312 406 tf
PA2334 406 tf
PA2359 406 tf
PA2423 406 tf
PA2489 406 tf
PA2588 406 tf
PA2846 406 tf
PA3583 406 tf
PA3845 406 tf
PA3932 406 tf
PA3995 406 tf
PA4185 406 tf
PA4436 406 tf
PA4508 406 tf
PA4530 406 tf
PA4703 406 tf
PA4831 406 tf
PA5032 406 tf
PA5374 406 tf
PA5506 406 tf
PA5525 406 tf

Warning: PA2359 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
3272 3.40e-22 aaAaAtact.AAa.aatATTt.ta
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3273 4.20e+00 TtatttaagGAATAa
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3636 3.50e-33 TtaAaAaAtaat.AAttaatAttT
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3637 2.80e-08 ttaTaTTctTT
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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 PA2359

PA2359 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
Module neighborhood information for PA2359

PA2359 has total of 26 gene neighbors in modules 222, 406
Gene neighbors (26)
Gene Common Name Description Module membership
PA0191 PA0191 probable transcriptional regulator (NCBI) 362, 406
PA0201 PA0201 hypothetical protein (NCBI) 222, 406
PA0280 cysA sulfate transport protein CysA (NCBI) 222, 406
PA0281 cysW sulfate transport protein CysW (NCBI) 222, 406
PA0282 cysT sulfate transport protein CysT (NCBI) 222, 406
PA0283 sbp sulfate-binding protein precursor (NCBI) 222, 406
PA0284 PA0284 hypothetical protein (NCBI) 222, 406
PA1493 cysP sulfate-binding protein of ABC transporter (NCBI) 222, 237
PA1756 cysH phosphoadenosine phosphosulfate reductase (NCBI) 222, 406
PA1837 PA1837 hypothetical protein (NCBI) 222, 406
PA1838 cysI sulfite reductase (NCBI) 222, 406
PA2062 PA2062 probable pyridoxal-phosphate dependent enzyme (NCBI) 222, 406
PA2083 PA2083 probable ring-hydroxylating dioxygenase subunit (NCBI) 222, 406
PA2202 PA2202 probable amino acid permease (NCBI) 362, 406
PA2203 PA2203 probable amino acid permease (NCBI) 362, 406
PA2204 PA2204 probable binding protein component of ABC transporter (NCBI) 222, 406
PA2310 PA2310 hypothetical protein (NCBI) 22, 406
PA2311 PA2311 hypothetical protein (NCBI) 22, 406
PA2359 PA2359 probable transcriptional regulator (NCBI) 222, 406
PA3446 PA3446 hypothetical protein (NCBI) 222, 406
PA3450 PA3450 probable antioxidant protein (NCBI) 222, 406
PA3931 PA3931 hypothetical protein (NCBI) 222, 406
PA3932 PA3932 probable transcriptional regulator (NCBI) 93, 406
PA4442 cysN binfunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein (NCBI) 222, 406
PA4443 cysD sulfate adenylyltransferase subunit 2 (NCBI) 222, 406
PA5024 PA5024 hypothetical protein (NCBI) 222, 406
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 PA2359
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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