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)
