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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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The Genetic Regulation Schematic for the E. coli torCAD operon.
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Figure 5: The Genetic Regulation Schematic for the E. coli torCAD operon.

Mentions: The Genetic Regulation Schematic, depicted in Figure 5, shows both direct and indirect regulators that affect the expression (transcription and translation) of a gene or set of related genes. The diagram appears on both gene and pathway pages. To the left are one or more boxes representing the set of genes in an operon or pathway. Transcription factors or other entities that regulate a gene are drawn as circular icons, with arrows pointing to the regulated entities (arrows that represent direct regulation of the targeted genes are drawn in green or magenta, depending on whether they activate or inhibit expression, respectively; arrows that represent dual or indirect regulation are always drawn in brown). The expression of these transcription factors (or other protein or RNA regulators) may in turn be regulated by other factors (or they may regulate their own expression), and these interactions are also shown. Thus a network is built up that indicates the complete cascade of expression-level regulatory effects.


Regulatory network operations in the Pathway Tools software.

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

The Genetic Regulation Schematic for the E. coli torCAD operon.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: The Genetic Regulation Schematic for the E. coli torCAD operon.
Mentions: The Genetic Regulation Schematic, depicted in Figure 5, shows both direct and indirect regulators that affect the expression (transcription and translation) of a gene or set of related genes. The diagram appears on both gene and pathway pages. To the left are one or more boxes representing the set of genes in an operon or pathway. Transcription factors or other entities that regulate a gene are drawn as circular icons, with arrows pointing to the regulated entities (arrows that represent direct regulation of the targeted genes are drawn in green or magenta, depending on whether they activate or inhibit expression, respectively; arrows that represent dual or indirect regulation are always drawn in brown). The expression of these transcription factors (or other protein or RNA regulators) may in turn be regulated by other factors (or they may regulate their own expression), and these interactions are also shown. Thus a network is built up that indicates the complete cascade of expression-level regulatory effects.

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