Organism : Pseudomonas aeruginosa | Module List :
PA1760

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (5)
Function System
ATP-dependent transcriptional regulator cog/ cog
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 PA1760
(Mouseover regulator name to see its description)

PA1760 is regulated by 57 influences and regulates 53 modules.
Regulators for PA1760 (57)
Regulator Module Operator
PA0367 239 tf
PA0424 239 tf
PA0533 239 tf
PA0652 239 tf
PA0708 239 tf
PA0764 239 tf
PA0784 239 tf
PA0797 239 tf
PA1015 239 tf
PA1099 239 tf
PA1159 239 tf
PA1285 239 tf
PA1713 239 tf
PA1759 239 tf
PA1760 239 tf
PA1853 239 tf
PA1949 239 tf
PA1978 239 tf
PA2010 239 tf
PA2016 239 tf
PA2020 239 tf
PA2267 239 tf
PA2332 239 tf
PA2376 239 tf
PA2577 239 tf
PA2713 239 tf
PA2917 239 tf
PA3215 239 tf
PA3249 239 tf
PA3771 239 tf
PA4185 239 tf
PA4436 239 tf
PA4659 239 tf
PA4755 239 tf
PA4769 239 tf
PA4787 239 tf
PA4853 239 tf
PA5288 239 tf
PA5337 239 tf
PA5380 239 tf
PA0179 252 tf
PA0784 252 tf
PA1128 252 tf
PA1759 252 tf
PA1760 252 tf
PA1978 252 tf
PA2047 252 tf
PA2121 252 tf
PA2123 252 tf
PA3622 252 tf
PA3921 252 tf
PA4703 252 tf
PA4745 252 tf
PA5059 252 tf
PA5380 252 tf
PA5506 252 tf
PA5511 252 tf

Warning: PA1760 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
3306 5.60e-21 cacaAtAAcaAtaA.aa
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3307 2.50e+02 AgacctctgTtatttta.CGtgA
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3332 7.70e-04 ATaaaTaaAaagAggaatatgC
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3333 5.40e-02 ATgcc.GTcTtaTcttggttaT
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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 PA1760

PA1760 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
ATP-dependent transcriptional regulator cog/ cog
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 PA1760

PA1760 has total of 36 gene neighbors in modules 239, 252
Gene neighbors (36)
Gene Common Name Description Module membership
PA0129 gabP gamma-aminobutyrate permease (NCBI) 145, 239
PA0743 PA0743 probable 3-hydroxyisobutyrate dehydrogenase (NCBI) 252, 503
PA0866 aroP2 aromatic amino acid transport protein AroP2 (NCBI) 239, 365
PA0887 acsA acetyl-coenzyme A synthetase (NCBI) 239, 491
PA1759 PA1759 probable transcriptional regulator (NCBI) 239, 252
PA1760 PA1760 probable transcriptional regulator (NCBI) 239, 252
PA1761 PA1761 hypothetical protein (NCBI) 252, 515
PA1984 PA1984 probable aldehyde dehydrogenase (NCBI) 239, 336
PA1991 PA1991 probable iron-containing alcohol dehydrogenase (NCBI) 239, 491
PA2002 PA2002 hypothetical protein (NCBI) 239, 365
PA2006 PA2006 probable major facilitator superfamily (MFS) transporter (NCBI) 239, 365
PA2121 PA2121 probable transcriptional regulator (NCBI) 252, 443
PA2122 PA2122 hypothetical protein (NCBI) 252, 294
PA2557 PA2557 acyl-CoA synthase (NCBI) 145, 239
PA3038 PA3038 probable porin (NCBI) 239, 491
PA3089 PA3089 hypothetical protein (NCBI) 252, 349
PA3186 oprB Glucose/carbohydrate outer membrane porin OprB precursor (NCBI) 239, 365
PA3187 PA3187 probable ATP-binding component of ABC transporter (NCBI) 239, 365
PA3188 PA3188 probable permease of ABC sugar transporter (NCBI) 239, 365
PA3189 PA3189 probable permease of ABC sugar transporter (NCBI) 239, 365
PA3190 PA3190 probable binding protein component of ABC sugar transporter (NCBI) 239, 365
PA3234 actP acetate permease (NCBI) 239, 491
PA3235 PA3235 hypothetical protein (NCBI) 239, 491
PA3250 PA3250 hypothetical protein (NCBI) 84, 252
PA3251 PA3251 hypothetical protein (NCBI) 84, 252
PA3710 PA3710 probable GMC-type oxidoreductase (NCBI) 142, 239
PA3921 PA3921 probable transcriptional regulator (NCBI) 252, 482
PA3922 PA3922 hypothetical protein (NCBI) 252, 515
PA3923 PA3923 hypothetical protein (NCBI) 252, 515
PA3924 PA3924 acyl-CoA synthase (NCBI) 252, 294
PA4023 PA4023 probable transport protein (NCBI) 239, 336
PA4024 eutB ethanolamine ammonia-lyase large subunit (NCBI) 239, 336
PA4025 PA4025 ethanolamine ammonia-lyase small subunit (NCBI) 239, 336
PA4733 acsB acetyl-coenzyme A synthetase (NCBI) 239, 365
PA5153 PA5153 probable periplasmic binding protein (NCBI) 193, 239
PA5380 PA5380 probable transcriptional regulator (NCBI) 239, 491
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 PA1760
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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