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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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A sample regulatory interaction editor dialog.
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Figure 2: A sample regulatory interaction editor dialog.

Mentions: Pathway Tools contains a full suite of form-based interactive editors for curation of regulation. The regulatory interaction editor allows the user to specify the class of regulation, the object being regulated, the regulator, and whether the regulation is activation or inhibition. There are fields for entering literature citations, evidence codes for the regulatory interaction, and a textual commentary. Depending on the class of regulation, additional fields enable the user to specify a binding site location, whether or not a protein regulator has a small molecule ligand, a mechanism, and/or other sites of interest, such as the anti-terminator and pause sites for attenuation interactions. An example editor is shown in Figure 2.


Regulatory network operations in the Pathway Tools software.

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

A sample regulatory interaction editor dialog.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: A sample regulatory interaction editor dialog.
Mentions: Pathway Tools contains a full suite of form-based interactive editors for curation of regulation. The regulatory interaction editor allows the user to specify the class of regulation, the object being regulated, the regulator, and whether the regulation is activation or inhibition. There are fields for entering literature citations, evidence codes for the regulatory interaction, and a textual commentary. Depending on the class of regulation, additional fields enable the user to specify a binding site location, whether or not a protein regulator has a small molecule ligand, a mechanism, and/or other sites of interest, such as the anti-terminator and pause sites for attenuation interactions. An example editor is shown in Figure 2.

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