PathSys

The PathSys System

PathSys is a graph-based system for creating a combined database of biological pathways, gene regulatory networks and protein interaction maps.

PathSys is a general-purpose, scalable warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping.

In PathSys are integrated over 14 curated and publicly contributed data sources for the 8 representative organisms (see list below), as well as Gene Ontology, which is structured as an acyclic graph.

The organisms are:

• Budding Yeast (Saccharomices cerevisiae)
• Schizosaccharomyces pombe
• Fly (Drosophila melanogaster)
• Caenorhabditis elegans
• Arabidopsis thaliana
• Mouse (Mus musculis)
• Human (Homo sapience)
• Zebrafish (Danio rerio)

The data sources are:

• Co-immunoprecipitation data (Gavin, A. C. et al. (2002) "Functional organization of the yeast proteome by systematic analysis of protein complexes". Nature, 415, 141147.)
• Co-immunoprecipitation data (Ho, Y. et al. (2002) "Systematic identification of protein complexes in saccharomyces cerevisiae by mass spectrometry". Nature, 415, 180183.)
• Yeast-two hybrid data (Ito, T. et al. (2001) "A comprehensive two-hybrid analysis to explore the yeast protein interactome". Proc Natl Acad Sci U S A. 98, 4569-74 . )
• Yeast-two hybrid data (Uetz, P. et al. (2000) "A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae". Nature 403,623-7.)
• Genetic interaction data (Tong, A. H. Y. et al. (2001) "Systematic genetic analysis with ordered arrays of yeast deletion mutants". Science, 294, 23642368.)
• Genetic interaction data (Tong, A.H. et al. "Global mapping of the yeast genetic interaction network". Science 303, 808-13 (2004).)
• MIT data http://web.wi.mit.edu/young/regulatory_network/, (Lee, T. et al. (2002) "Transcriptional regulatory networks in Saccharomyces cerevisiae". Science, 298, 799804.)
• UCSF localization data (Huh, W.K. et al. (2003), "Global analysis of protein localization in budding yeast". Nature 425,686-91.)
• MIPS data (http://mips.gsf.de/genre/proj/yeast/)
• CSH data (http://rulai.cshl.edu/SCPD/)
• Transfac (http://www.gene-regulation.com/)
• BIND database (http://bind.ca/)
• pre-BIND database (http://www.blueprint.org/products/prebind/)
• KEGG (http://www.genome.ad.jp/kegg)