Download - Yeast Biochemical Pathways Tool
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Yeast Biochemical Pathways Tool
Rama BalakrishnanSGD
Stanford University
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About S. cerevisiae
• Simplest eukaryotic unicellular organism• Its power:
– Model organism to study genetics, cellular processes
– Several industrial applications
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About SGDOnline database for the genomic sequence, genetics and molecular biology of Saccharomyces
cerevisiae, commonly known as baker’s or budding yeast.
6604 protein coding genes
http://www.yeastgenome.org
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Lysine Biosynthesis from KEGG
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Building Yeast Biochemical Pathways
• Used GO Function ontology annotations– EC2GO mapping
• Gene product or Description field information– Matches ‘ase’, manual mapping
• Initial build done with 731 genes• We have 6604 protein coding genes in
the database
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Summary Total number of genes: 731
EC # matches: 635
Function name matches: 17(no E.C. available)
Failed matches: 79(many turned out to be protein kinases, tRNA modifcation, or egosterolbiosynthesis genes)
Pathways Predicted: 125
Reactions mapped: 652
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� I nitial Cleanup after Build
• Resolve ambiguous EC numbers• Fill in missing reactions• Delete pathways that don’t occur in
yeast• Add pathways unique to yeast• Contribute new pathways to MetaCyc
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Curation
• Types of pathway information captured:– References– Summary paragraph– Evidence code– Reactions; EC numbers– Genes and gene product references
• Compound IDs from KEGG, CheBI, PubChem
Current Statistics: 154 pathways, 460 genes
Available for download from our FTP site
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Curated Pathway
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How did we integrate Pathways with other resources?
From the home page, from Quick Search box, from individual locuspages
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Quick search results
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Yeast Biochemical Pathways
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From the Locus Summary Pages
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Lysine Biosynthesis from KEGG
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Lysine Biosynthesis - Detailed View