Organism : Pseudomonas aeruginosa | Module List :
PA4937 rnr

exoribonuclease RNase R (NCBI)

CircVis
Functional Annotations (8)
Function System
Exoribonuclease R cog/ cog
RNA binding go/ molecular_function
ribonuclease activity go/ molecular_function
RNA metabolic process go/ biological_process
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
RNA degradation kegg/ kegg pathway
3_prime_RNase tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4937
(Mouseover regulator name to see its description)

PA4937 is regulated by 42 influences and regulates 0 modules.
Regulators for PA4937 rnr (42)
Regulator Module Operator
PA0125 381 tf
PA0236 381 tf
PA0393 381 tf
PA2047 381 tf
PA2737 381 tf
PA3458 381 tf
PA3622 381 tf
PA3879 381 tf
PA4269 381 tf
PA4462 381 tf
PA4493 381 tf
PA5253 381 tf
PA5437 381 tf
PA0125 191 tf
PA0167 191 tf
PA0272 191 tf
PA0393 191 tf
PA0514 191 tf
PA0890 191 tf
PA0893 191 tf
PA1229 191 tf
PA1335 191 tf
PA1760 191 tf
PA1912 191 tf
PA1980 191 tf
PA2016 191 tf
PA2096 191 tf
PA2547 191 tf
PA2591 191 tf
PA2737 191 tf
PA2957 191 tf
PA3225 191 tf
PA3364 191 tf
PA3864 191 tf
PA3895 191 tf
PA4169 191 tf
PA4269 191 tf
PA4270 191 tf
PA4493 191 tf
PA5166 191 tf
PA5253 191 tf
PA5483 191 tf

Warning: PA4937 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
3210 1.50e+01 AggaGAaaAc
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3211 1.30e+03 gttggCGCTataacA
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3586 1.60e+03 GaAGA.Aa
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3587 6.60e+03 TTGaTTaaTGcCTGaTTATT
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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 PA4937

PA4937 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Exoribonuclease R cog/ cog
RNA binding go/ molecular_function
ribonuclease activity go/ molecular_function
RNA metabolic process go/ biological_process
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
RNA degradation kegg/ kegg pathway
3_prime_RNase tigr/ tigrfam
Module neighborhood information for PA4937

PA4937 has total of 38 gene neighbors in modules 191, 381
Gene neighbors (38)
Gene Common Name Description Module membership
PA0068 PA0068 hypothetical protein (NCBI) 191, 293
PA0130 PA0130 probable aldehyde dehydrogenase (NCBI) 145, 191
PA0131 PA0131 hypothetical protein (NCBI) 145, 191
PA0132 PA0132 beta-alanine--pyruvate transaminase (NCBI) 145, 191
PA0337 ptsP phosphoenolpyruvate-protein phosphotransferase PtsP (NCBI) 191, 264
PA0399 PA0399 cystathionine beta-synthase (NCBI) 35, 191
PA0400 PA0400 probable cystathionine gamma-lyase (NCBI) 35, 191
PA0660 PA0660 hypothetical protein (NCBI) 7, 381
PA0830 PA0830 hypothetical protein (NCBI) 191, 381
PA0896 aruF arginine/ornithine succinyltransferase AI subunit (NCBI) 191, 380
PA0897 aruG arginine/ornithine succinyltransferase AII subunit (NCBI) 191, 380
PA0898 aruD succinylglutamate 5-semialdehyde dehydrogenase (NCBI) 191, 380
PA0899 aruB succinylarginine dihydrolase (NCBI) 191, 380
PA2290 gcd glucose dehydrogenase (NCBI) 191, 381
PA2318 PA2318 hypothetical protein (NCBI) 189, 381
PA2323 PA2323 probable glyceraldehyde-3-phosphate dehydrogenase (NCBI) 191, 505
PA3120 leuD isopropylmalate isomerase small subunit (NCBI) 381, 477
PA3121 leuC isopropylmalate isomerase large subunit (NCBI) 381, 477
PA3529 PA3529 probable peroxidase (NCBI) 88, 381
PA3628 PA3628 probable esterase (NCBI) 381, 488
PA3629 adhC alcohol dehydrogenase class III (NCBI) 381, 488
PA3792 leuA 2-isopropylmalate synthase (RefSeq) 381, 488
PA3882 PA3882 hypothetical protein (NCBI) 203, 381
PA3919 PA3919 hypothetical protein (NCBI) 141, 381
PA4329 pykA pyruvate kinase (NCBI) 237, 381
PA4336 PA4336 hypothetical protein (NCBI) 381, 436
PA4576 PA4576 probable ATP-dependent protease (NCBI) 191, 540
PA4579 PA4579 hypothetical protein (NCBI) 49, 191
PA4615 PA4615 probable oxidoreductase (NCBI) 191, 291
PA4732 pgi glucose-6-phosphate isomerase (NCBI) 381, 488
PA4808 selA selenocysteine synthase (NCBI) 381, 540
PA4810 fdnI nitrate-inducible formate dehydrogenase, gamma subunit (NCBI) 381, 505
PA4811 fdnH nitrate-inducible formate dehydrogenase, beta subunit (NCBI) 381, 505
PA4812 fdnG formate dehydrogenase-O (NCBI) 381, 505
PA4936 PA4936 probable rRNA methylase (NCBI) 191, 381
PA4937 rnr exoribonuclease RNase R (NCBI) 191, 381
PA5496 PA5496 hypothetical protein (NCBI) 191, 462
PA5497 PA5497 hypothetical protein (NCBI) 191, 462
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 PA4937
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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