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Regulatory network operations in the Pathway Tools software.

Paley SM, Latendresse M, Karp PD - BMC Bioinformatics (2012)

Bottom Line: We introduce a novel type of enrichment analysis that asks whether a gene-expression dataset is over-represented for known regulators.We present algorithms for ranking the degree of regulatory influence of genes, and for computing the net positive and negative regulatory influences on a gene.Pathway Tools provides a comprehensive environment for manipulating molecular regulatory interactions that integrates regulatory data with an organism's genome and metabolic network.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Research Group, SRI International 333 Ravenswood Ave, Menlo Park, CA 94025, USA.

ABSTRACT

Background: Biologists are elucidating complex collections of genetic regulatory data for multiple organisms. Software is needed for such regulatory network data.

Results: The Pathway Tools software supports storage and manipulation of regulatory information through a variety of strategies. The Pathway Tools regulation ontology captures transcriptional and translational regulation, substrate-level regulation of enzyme activity, post-translational modifications, and regulatory pathways. Regulatory visualizations include a novel diagram that summarizes all regulatory influences on a gene; a transcription-unit diagram, and an interactive visualization of a full transcriptional regulatory network that can be painted with gene expression data to probe correlations between gene expression and regulatory mechanisms. We introduce a novel type of enrichment analysis that asks whether a gene-expression dataset is over-represented for known regulators. We present algorithms for ranking the degree of regulatory influence of genes, and for computing the net positive and negative regulatory influences on a gene.

Conclusions: Pathway Tools provides a comprehensive environment for manipulating molecular regulatory interactions that integrates regulatory data with an organism's genome and metabolic network. Curated collections of regulatory data authored using Pathway Tools are available for Escherichia coli, Bacillus subtilis, and Shewanella oneidensis.

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Related in: MedlinePlus

Regulatory Overviews of E. coli;  elliptical (upper) and layered (below) layouts are shown. The user has not yet requested display of arrows that show regulatory relationships.
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Figure 6: Regulatory Overviews of E. coli; elliptical (upper) and layered (below) layouts are shown. The user has not yet requested display of arrows that show regulatory relationships.

Mentions: Two alternative layouts, shown in Figure 6, are supported. The upper elliptical layout shows all transcription factors and sigma factors in two inner ellipses, with all regulated genes that are not regulators in an outer ellipse. The lower, layered layout shows all transcription factors and sigma factors in the top layers, with all regulated genes that are not regulators in the lowest layer. The elliptical layout is designed to show the global regulatory network; the layered layout is designed to show smaller regulatory subnetworks.


Regulatory network operations in the Pathway Tools software.

Paley SM, Latendresse M, Karp PD - BMC Bioinformatics (2012)

Regulatory Overviews of E. coli;  elliptical (upper) and layered (below) layouts are shown. The user has not yet requested display of arrows that show regulatory relationships.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3473263&req=5

Figure 6: Regulatory Overviews of E. coli; elliptical (upper) and layered (below) layouts are shown. The user has not yet requested display of arrows that show regulatory relationships.
Mentions: Two alternative layouts, shown in Figure 6, are supported. The upper elliptical layout shows all transcription factors and sigma factors in two inner ellipses, with all regulated genes that are not regulators in an outer ellipse. The lower, layered layout shows all transcription factors and sigma factors in the top layers, with all regulated genes that are not regulators in the lowest layer. The elliptical layout is designed to show the global regulatory network; the layered layout is designed to show smaller regulatory subnetworks.

Bottom Line: We introduce a novel type of enrichment analysis that asks whether a gene-expression dataset is over-represented for known regulators.We present algorithms for ranking the degree of regulatory influence of genes, and for computing the net positive and negative regulatory influences on a gene.Pathway Tools provides a comprehensive environment for manipulating molecular regulatory interactions that integrates regulatory data with an organism's genome and metabolic network.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Research Group, SRI International 333 Ravenswood Ave, Menlo Park, CA 94025, USA.

ABSTRACT

Background: Biologists are elucidating complex collections of genetic regulatory data for multiple organisms. Software is needed for such regulatory network data.

Results: The Pathway Tools software supports storage and manipulation of regulatory information through a variety of strategies. The Pathway Tools regulation ontology captures transcriptional and translational regulation, substrate-level regulation of enzyme activity, post-translational modifications, and regulatory pathways. Regulatory visualizations include a novel diagram that summarizes all regulatory influences on a gene; a transcription-unit diagram, and an interactive visualization of a full transcriptional regulatory network that can be painted with gene expression data to probe correlations between gene expression and regulatory mechanisms. We introduce a novel type of enrichment analysis that asks whether a gene-expression dataset is over-represented for known regulators. We present algorithms for ranking the degree of regulatory influence of genes, and for computing the net positive and negative regulatory influences on a gene.

Conclusions: Pathway Tools provides a comprehensive environment for manipulating molecular regulatory interactions that integrates regulatory data with an organism's genome and metabolic network. Curated collections of regulatory data authored using Pathway Tools are available for Escherichia coli, Bacillus subtilis, and Shewanella oneidensis.

Show MeSH
Related in: MedlinePlus