Organism : Pseudomonas aeruginosa | Module List :
PA2005

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (9)
Function System
Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
signal transducer activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
signal transduction go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2005
(Mouseover regulator name to see its description)

PA2005 is regulated by 25 influences and regulates 8 modules.
Regulators for PA2005 (25)
Regulator Module Operator
PA0218 489 tf
PA1261 489 tf
PA1399 489 tf
PA2005 489 tf
PA2766 489 tf
PA3027 489 tf
PA3420 489 tf
PA3596 489 tf
PA4238 489 tf
PA4270 489 tf
PA4914 489 tf
PA5032 489 tf
PA5389 489 tf
PA0701 241 tf
PA1153 241 tf
PA1223 241 tf
PA1261 241 tf
PA2005 241 tf
PA2050 241 tf
PA3381 241 tf
PA3433 241 tf
PA4341 241 tf
PA4914 241 tf
PA5032 241 tf
PA5431 241 tf

Warning: PA2005 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
3310 3.80e+04 CGgaTaccCCAGatactC.CG
Loader icon
3311 2.80e+04 AcGccT.TCctCacTG
Loader icon
3792 2.00e-05 GaAcCTTTcctccTgCtaaTgccA
Loader icon
3793 3.20e-03 TGacACcGATCAAGacAtacGaCA
Loader icon
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 PA2005

PA2005 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
signal transducer activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
signal transduction go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
Module neighborhood information for PA2005

PA2005 has total of 46 gene neighbors in modules 241, 489
Gene neighbors (46)
Gene Common Name Description Module membership
PA0223 PA0223 probable dihydrodipicolinate synthetase (NCBI) 175, 489
PA0224 PA0224 hypothetical protein (NCBI) 401, 489
PA0225 PA0225 probable transcriptional regulator (NCBI) 58, 489
PA0311 PA0311 hypothetical protein (NCBI) 16, 489
PA0602 PA0602 probable binding protein component of ABC transporter (NCBI) 31, 241
PA0673 PA0673 hypothetical protein (NCBI) 489, 500
PA0714 PA0714 hypothetical protein (NCBI) 241, 311
PA0742 PA0742 hypothetical protein (NCBI) 246, 489
PA0847 PA0847 hypothetical protein (NCBI) 241, 523
PA0850 PA0850 hypothetical protein (NCBI) 483, 489
PA1046 PA1046 hypothetical protein (NCBI) 241, 375
PA1133 PA1133 hypothetical protein (NCBI) 171, 241
PA1153 PA1153 hypothetical protein (NCBI) 104, 241
PA1234 PA1234 hypothetical protein (NCBI) 20, 241
PA1284 PA1284 probable acyl-CoA dehydrogenase (NCBI) 408, 489
PA1636 kdpD two-component sensor KdpD (NCBI) 241, 313
PA1637 kdpE two-component response regulator KdpE (NCBI) 241, 313
PA1762 PA1762 hypothetical protein (NCBI) 443, 489
PA1764 PA1764 hypothetical protein (NCBI) 92, 489
PA1906 PA1906 hypothetical protein (NCBI) 175, 489
PA2005 PA2005 probable transcriptional regulator (NCBI) 241, 489
PA2596 PA2596 hypothetical protein (NCBI) 241, 497
PA2863 lipH lipase chaperone (NCBI) 246, 489
PA2893 PA2893 acyl-CoA synthase (NCBI) 330, 489
PA3024 PA3024 probable carbohydrate kinase (NCBI) 246, 489
PA3025 PA3025 probable FAD-dependent glycerol-3-phosphate dehydrogenase (NCBI) 246, 489
PA3026 PA3026 hypothetical protein (NCBI) 28, 489
PA3027 PA3027 probable transcriptional regulator (NCBI) 170, 489
PA3325 PA3325 hypothetical protein (NCBI) 489, 545
PA3358 PA3358 hypothetical protein (NCBI) 171, 241
PA3534 PA3534 probable oxidoreductase (NCBI) 483, 489
PA3669 PA3669 hypothetical protein (NCBI) 104, 241
PA3670 PA3670 hypothetical protein (NCBI) 104, 241
PA3780 PA3780 hypothetical protein (NCBI) 16, 489
PA3781 PA3781 probable transporter (NCBI) 16, 489
PA3783 PA3783 hypothetical protein (NCBI) 175, 241
PA3886 PA3886 hypothetical protein (NCBI) 187, 241
PA3953 PA3953 hypothetical protein (NCBI) 171, 489
PA4093 PA4093 hypothetical protein (NCBI) 241, 489
PA4347 PA4347 hypothetical protein (NCBI) 241, 253
PA4592 PA4592 probable outer membrane protein precursor (NCBI) 313, 489
PA4921 PA4921 hypothetical protein (NCBI) 206, 241
PA5089 PA5089 hypothetical protein (NCBI) 241, 473
PA5283 PA5283 probable transcriptional regulator (NCBI) 241, 434
PA5444 PA5444 hypothetical protein (NCBI) 206, 241
PA5514 poxB probable beta-lactamase (NCBI) 241, 469
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 PA2005
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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