Organism : Pseudomonas aeruginosa | Module List :
PA0403 pyrR

pyrimidine regulatory protein PyrR (NCBI)

CircVis
Functional Annotations (5)
Function System
Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase cog/ cog
uracil phosphoribosyltransferase activity go/ molecular_function
nucleoside metabolic process go/ biological_process
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0403
(Mouseover regulator name to see its description)

PA0403 is regulated by 53 influences and regulates 0 modules.
Regulators for PA0403 pyrR (53)
Regulator Module Operator
PA0163 47 tf
PA0279 47 tf
PA0393 47 tf
PA0448 47 tf
PA0512 47 tf
PA0576 47 tf
PA0652 47 tf
PA1099 47 tf
PA1998 47 tf
PA2020 47 tf
PA2050 47 tf
PA2126 47 tf
PA3002 47 tf
PA3225 47 tf
PA3879 47 tf
PA4070 47 tf
PA4269 47 tf
PA4270 47 tf
PA4493 47 tf
PA4755 47 tf
PA5125 47 tf
PA5166 47 tf
PA5253 47 tf
PA0125 167 tf
PA0393 167 tf
PA0448 167 tf
PA0527 167 tf
PA0652 167 tf
PA0893 167 tf
PA1455 167 tf
PA1836 167 tf
PA2020 167 tf
PA2115 167 tf
PA2126 167 tf
PA2846 167 tf
PA2921 167 tf
PA3002 167 tf
PA3027 167 tf
PA3133 167 tf
PA3322 167 tf
PA3458 167 tf
PA3563 167 tf
PA3879 167 tf
PA3973 167 tf
PA4080 167 tf
PA4132 167 tf
PA4269 167 tf
PA4493 167 tf
PA4902 167 tf
PA5125 167 tf
PA5166 167 tf
PA5253 167 tf
PA5324 167 tf

Warning: PA0403 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
2926 2.20e+01 tagctaTttT.CcT
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2927 1.40e+03 tttcGGatgtT
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3162 4.60e+02 AggtAaaTgcgtcaCTtgT
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3163 2.80e+02 AaAaaGtT.ta.gCCCtcAt
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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 PA0403

PA0403 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase cog/ cog
uracil phosphoribosyltransferase activity go/ molecular_function
nucleoside metabolic process go/ biological_process
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for PA0403

PA0403 has total of 22 gene neighbors in modules 47, 167
Gene neighbors (22)
Gene Common Name Description Module membership
PA0401 pyrC dihydroorotase (NCBI) 47, 225
PA0402 pyrB aspartate carbamoyltransferase catalytic subunit (NCBI) 47, 225
PA0403 pyrR pyrimidine regulatory protein PyrR (NCBI) 47, 167
PA0426 mexB Resistance-Nodulation-Cell Division (RND) multidrug efflux transporter MexB (NCBI) 47, 509
PA0427 oprM Major intrinsic multiple antibiotic resistance efflux outer membrane protein OprM precursor (NCBI) 47, 509
PA0835 pta phosphate acetyltransferase (NCBI) 38, 167
PA0836 PA0836 probable acetate kinase (NCBI) 167, 416
PA1550 PA1550 hypothetical protein (NCBI) 46, 167
PA1551 PA1551 probable ferredoxin (NCBI) 46, 167
PA1561 aer aerotaxis receptor Aer (NCBI) 47, 167
PA2612 serS seryl-tRNA synthetase (NCBI) 47, 121
PA4464 ptsN nitrogen regulatory IIA protein (NCBI) 167, 430
PA4465 PA4465 hypothetical protein (NCBI) 167, 430
PA5015 aceE pyruvate dehydrogenase (NCBI) 47, 213
PA5016 aceF dihydrolipoamide acetyltransferase (NCBI) 47, 213
PA5119 glnA glutamine synthetase (NCBI) 47, 167
PA5242 ppk polyphosphate kinase (NCBI) 47, 167
PA5243 hemB delta-aminolevulinic acid dehydratase (NCBI) 47, 167
PA5346 PA5346 hypothetical protein (NCBI) 2, 167
PA5435 PA5435 oxaloacetate decarboxylase (NCBI) 47, 179
PA5436 PA5436 acetyl-CoA carboxylase (NCBI) 47, 179
PA5495 thrB homoserine kinase (NCBI) 167, 452
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 PA0403
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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