BiologicalNetworks BiologicalNetworks

Database

BiologicalNetworks Database

BiologicalNetworks database (IntegromeDB) integrates over 100 curated and publicly contributed data sources and provides functional, genetic, genomic, transcriptomic and proteomic information. Information featured in the database includes gene function, pathways, protein-protein interactions, gene expression, orthologies, mutations and SNPs, disease relationships, related drugs and compounds.

 

Representative organisms are:
  • Budding Yeast (Saccharomices cerevisiae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fly (Drosophila melanogaster)
  • Caenorhabditis elegans
  • Arabidopsis thaliana
  • Mouse (Mus musculis)
  • Human (Homo sapiens)
  • Zebrafish (Danio rerio)
Representative data sources are:
  • MIPS data (http://mips.gsf.de/genre/proj/yeast/)
  • KEGG (http://www.genome.ad.jp/kegg)
  • Transfac (http://www.gene-regulation.com/)
  • BIND database (http://bind.ca/)
  • pre-BIND database (http://www.blueprint.org/products/prebind/)
  • CSH data (http://rulai.cshl.edu/SCPD/)
  • MIT transcriptional data (Lee, T. et al. (2002) "Transcriptional regulatory networks in Saccharomyces cerevisiae". Science, 298, 799804.) http://web.wi.mit.edu/young/regulatory_network/
  • UCSF localization data (Huh, W.K. et al. (2003), "Global analysis of protein localization in budding yeast". Nature 425,686-91.)
  • 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).)