title: Regulatory network operations in the Pathway Tools software.
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.
authors.affiliation: Bioinformatics Research Group, SRI International 333 Ravenswood Ave, Menlo Park, CA 94025, USA.
authors.forename: Suzanne M
authors.initials: SM
authors.lastname: Paley
authors.forename: Mario
authors.initials: M
authors.lastname: Latendresse
authors.forename: Peter D
authors.initials: PD
authors.lastname: Karp
mesh_terms: D000465:Algorithms; D001412:Bacillus subtilis / Q000235:genetics; D004798:Enzymes / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D016678:Genome; D053858:Metabolic Networks and Pathways / Q000235:genetics; D014176:Protein Biosynthesis; D011499:Protein Processing, Post-Translational; D020592:Shewanella / Q000235:genetics; D012984:Software; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D004798:Enzymes; D014157:Transcription Factors