Proteome informatics, YMU

Pathways

Gene Ontology^TM (GO)

• Gene Ontology Consortium 
• GO browser (mirror site at YMU)

Classfied by organisms or by genes

• Yeast pathways
• Gene Networks Database (GeNet)
• BioCyc Knowledge Library (contains 13 microorganisms)
  • Query page: http://biocyc.org/
  • Ref for PathoLogic program: http://www.ai.sri.com/pkarp/pubs/99trbiotech.pdf 

Classified by functions

• Signal transduction pathways
  • Biocarta (簡介)
  • Signal Transduction Knowledge Environment (STKE)
  • Signaling PAthway database (SPAD)
  • Cell Signaling Network DataBase (CSNDB)
  • Transpath (commercial): describes signal transduction from the ligand at the surface of a cell up to the transcription factor
• Regulatory pathways
  • Kyoto Encyclopedia of Genes and Genomes (KEGG, mirror site at YMU)
  • aMaze database (an ongoing project)
• Metabolic pathways
  • aMaze database (an ongoing project)
  • Kyoto Encyclopedia of Genes and Genomes (KEGG, mirror site at at YMU)
  • BM's biochemical pathways
  • Enzyme database (BRENDA)
  • What is there (WIT)
  • Enzymes and Metabolic Pathways database  (EMP)
  • PathDB at National Center for Genome Resource

Portal site for pathways

• NAR's molecular biology databases

Organization

• The biopathways consortium

Last updated on Apr. 24, 2002 by ymbc@ym.edu.tw