Bioinformatics Approach: Understanding Genomic-Pathway-Chemical Connections with KEGG, Study notes of Biology

Download Bioinformatics Approach: Understanding Genomic-Pathway-Chemical Connections with KEGG and more Study notes Biology in PDF only on Docsity! Bioinformatics Approach To Chemical Genomics Minoru Kanehisa Institute of Chemical Research Kyoto University Outline Management of large scale bata Building blocks to biological Systems Linking biological system & environment New Approach Drug Target Perturbant Perturbed System Kyoto Encyclopedia Genes & Genomes (KEGG) KEGG Pathways & Networks Genes Ligands System Space Collection of 20+ databases KEGG Disease: arriving Jan 2008 KEGG Databases Database KEGG PATHWAY KEGG BRITE KEGG MODULE KEGG DISEASE KEGG ORTHOLOGY KEGG GENES KEGG DGENES KEGG EGENES KEGG GENOME KEGG SSDB KEGG COMPOUND KEGG DRUG KEGG GLYCAN KEGG ENZYME KEGG REACTION KEGG RPAIR Content Pathway maps Functional hierarchies Pathway modules (to be released) Diseases (to be released} KEGG orthology (KO} groups Genes in high-quality genomes Genes in draft genomes Genes as EST contigs Organisms with complete genomes Sequence similarities and best hit relations Metabolites Drugs Glycans Enzymes Enzymatic reactions Reactant pairs and chemical transformations  KEGG ontology (KO) K-number KEGG Pathway node + BRITE hierarchy node Over 700 genes Gene Dgenes: Draft Genes Egenes: ESTs Over 10,000 KO Groups What Next? Linking Gene expression Profile to Reaction Pattern profile Co-expression of genes Co-occurrence score to adjoining reaction Chemical Annotation in KEGG Linking exogenous chemical subsances to genomes. Chemical Structure Similarity Comparison of bit representation vectors (fingureprints) Comparison of graph objects Chemical Building blocks Conserved substances: Building blocks of compounds Variable substances: Reactions Interaction prediction/ network prediction Network models