AnIntroductiontoPathwayBioinformatics.ppt

An Introduction to Pathway Bioinformatics Yuanhua Tom Tang, Ph.D. Bioinformatics R D Hyseq Pharmaceuticals, Inc. Sunnyvale, CA, USA Singapore National University January, 2002 Definition of Bioinformatics Theoretical The essence of life is information. Bioinformatics is the study of the information content of life. Practical The essential tool is computer. Bioinformatics is computer-based information abstraction and processing of biological knowledge. Pathways A schematic diagram of a protein-protein or protein-molecule interaction pathway Pathway Database --Increasing Level of Complexity The genome 4 bases 3 billion bp total 3 billion bp/cell, identical The proteome 20 amino acids ~60K genes, ~200K proteins ~10K proteins/cell; different cells/conditions, different expressions The pathome ~200K reactions ~20K pathways ~1K pathways/cell; different cells/conditions, different expressions The Need for Pathway Informatics Good angle for data integration and representation. Research tool for scientists. Learning tool for students. Pharmaceutical drug discovery efforts would benefit from comprehensive pathway databases and tools. A challenge for post-genomic era List of Pathway Databases/Tools Name: KEGG (Kyoto Encyclopedia of Genes and Genomes) Web: http://www.genome.ad.jp/kegg/ Owner: Institute for Chemical Research, Kyoto University Description: KEGG is an effort to computerize current knowledge of molecular and cellular biology in terms of the information pathways that consist of interacting molecules or genes and to provide links from the gene catalogs produced by genome sequencing projects. The KEGG project is undertaken in the Bioinformatics Center, Institute for Chemical Research, Kyoto Univ. Name: PathDB Web: /pathdb/index.html Owner: National Center for Genomic Resources Description: PathDB? is a functional prototype research tool for biochemistry and functional genomics. One of the key underlying philosophies