Organism : Pseudomonas aeruginosa | Module List :
PA0155 pcaR

transcriptional regulator PcaR (NCBI)

CircVis
Functional Annotations (7)
Function System
Transcriptional regulator cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
transcription activator activity go/ molecular_function
positive regulation of transcription, DNA-dependent go/ biological_process
protocatechuate metabolic process go/ biological_process
pcaR_pcaU tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0155
(Mouseover regulator name to see its description)

PA0155 is regulated by 39 influences and regulates 18 modules.
Regulators for PA0155 pcaR (39)
Regulator Module Operator
PA0116 306 tf
PA0155 306 tf
PA0455 306 tf
PA0707 306 tf
PA1241 306 tf
PA1627 306 tf
PA2556 306 tf
PA2737 306 tf
PA2957 306 tf
PA3002 306 tf
PA3269 306 tf
PA3604 306 tf
PA3622 306 tf
PA3757 306 tf
PA3778 306 tf
PA3804 306 tf
PA4052 306 tf
PA4057 306 tf
PA4451 306 tf
PA5342 306 tf
PA0116 143 tf
PA1269 143 tf
PA1520 143 tf
PA1859 143 tf
PA2047 143 tf
PA2877 143 tf
PA2930 143 tf
PA3574 143 tf
PA3927 143 tf
PA3965 143 tf
PA4052 143 tf
PA4157 143 tf
PA4451 143 tf
PA4745 143 tf
PA4755 143 tf
PA4764 143 tf
PA4853 143 tf
PA5344 143 tf
PA5403 143 tf

Warning: PA0155 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
3116 2.10e+02 GgTAgAaTccgcgcccttT
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3117 1.60e+03 CgatGgaaacgGGc
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3438 9.00e-01 agGCAacgaagAc.a.gGaAaGCG
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3439 2.00e+00 GATAGGcatAatTCTgCcagA
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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 PA0155

PA0155 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Transcriptional regulator cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
transcription activator activity go/ molecular_function
positive regulation of transcription, DNA-dependent go/ biological_process
protocatechuate metabolic process go/ biological_process
pcaR_pcaU tigr/ tigrfam
Module neighborhood information for PA0155

PA0155 has total of 53 gene neighbors in modules 143, 306
Gene neighbors (53)
Gene Common Name Description Module membership
PA0015 PA0015 hypothetical protein (NCBI) 65, 143
PA0042 PA0042 hypothetical protein (NCBI) 143, 165
PA0148 PA0148 adenosine deaminase (NCBI) 276, 306
PA0155 pcaR transcriptional regulator PcaR (NCBI) 143, 306
PA0313 PA0313 probable permease of ABC transporter (NCBI) 268, 306
PA0361 PA0361 probable gamma-glutamyltranspeptidase precursor (NCBI) 306, 511
PA0455 dbpA RNA helicase DbpA (NCBI) 306, 517
PA0584 cca tRNA nucleotidyl transferase (NCBI) 245, 306
PA0976 PA0976 hypothetical protein (NCBI) 135, 143
PA1142 PA1142 probable transcriptional regulator (NCBI) 306, 528
PA1269 PA1269 probable transcriptional regulator (NCBI) 59, 143
PA1294 rnd ribonuclease D (NCBI) 306, 544
PA1520 PA1520 probable transcriptional regulator (NCBI) 143, 165
PA1627 PA1627 probable transcriptional regulator (NCBI) 306, 438
PA1644 PA1644 hypothetical protein (NCBI) 8, 143
PA1678 PA1678 probable DNA methylase (NCBI) 1, 306
PA1846 cti cis/trans isomerase (NCBI) 249, 306
PA2720 PA2720 hypothetical protein (NCBI) 306, 337
PA2765 PA2765 hypothetical protein (NCBI) 123, 306
PA2801 PA2801 hypothetical protein (NCBI) 306, 374
PA2930 PA2930 probable transcriptional regulator (NCBI) 143, 373
PA2980 PA2980 hypothetical protein (NCBI) 143, 165
PA2983 PA2983 probable tolQ-type transport protein (NCBI) 143, 490
PA2988 PA2988 hypothetical protein (NCBI) 103, 306
PA3048 PA3048 hypothetical protein (NCBI) 126, 306
PA3400 PA3400 hypothetical protein (NCBI) 306, 374
PA3490 PA3490 electron transport complex protein RnfB (NCBI) 306, 396
PA3574 PA3574 probable transcriptional regulator (NCBI) 143, 544
PA3675 PA3675 hypothetical protein (NCBI) 114, 143
PA3950 PA3950 probable ATP-dependent RNA helicase (NCBI) 143, 315
PA3951 PA3951 hypothetical protein (NCBI) 212, 306
PA3961 PA3961 probable ATP-dependent helicase (NCBI) 26, 306
PA4439 trpS tryptophanyl-tRNA synthetase (NCBI) 271, 306
PA4448 hisD histidinol dehydrogenase (NCBI) 306, 353
PA4524 nadC nicotinate-nucleotide pyrophosphorylase (NCBI) 306, 477
PA4609 radA DNA repair protein RadA (NCBI) 306, 438
PA4815 PA4815 hypothetical protein (NCBI) 143, 377
PA4945 miaA tRNA delta(2)-isopentenylpyrophosphate transferase (NCBI) 306, 478
PA4948 PA4948 hypothetical protein (NCBI) 86, 306
PA4949 PA4949 hypothetical protein (NCBI) 86, 306
PA4950 PA4950 hypothetical protein (NCBI) 86, 306
PA4952 PA4952 ribosome-associated GTPase (NCBI) 306, 501
PA5019 PA5019 hypothetical protein (NCBI) 143, 229
PA5021 PA5021 potassium/proton antiporter (RefSeq) 299, 306
PA5076 PA5076 probable binding protein component of ABC transporter (NCBI) 143, 234
PA5133 PA5133 hypothetical protein (NCBI) 103, 306
PA5215 gcvT1 aminomethyltransferase (NCBI) 143, 315
PA5225 PA5225 hypothetical protein (NCBI) 170, 306
PA5244 PA5244 hypothetical protein (NCBI) 103, 306
PA5333 PA5333 hypothetical protein (NCBI) 143, 232
PA5347 PA5347 hypothetical protein (NCBI) 143, 251
PA5358 ubiA 4-hydroxybenzoate octaprenyltransferase (NCBI) 143, 332
PA5519 PA5519 hypothetical protein (NCBI) 143, 368
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 PA0155
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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