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Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis

Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Winzeler, et al. Review - libraries. Genomic cDNA Other What are the advantages and disadvantages of each?

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Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis

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  1. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis Winzeler, et al.

  2. Review - libraries • Genomic • cDNA • Other • What are the advantages and disadvantages of each? • How do the different kinds of plasmids allow you to ask different questions with these libraries?

  3. Gene Replacement: • Have gene or know sequence • homologous gene replacement • how do you know you have replaced the gene? • markers • advantages • what else might you need? • challenges with other eukaryotes

  4. Genomics • Need genome-scale reagents • May be international and, for sure, multi-lab effort • Highthroughput

  5. 14 labs worked on this project

  6. What are some of the questions? • How many essential genes? • What are other common phenotypes? • What are all the genes in pathway x? • Can we develop methods to measure subtle effects of competition? Barcodes • What are other questions?

  7. Barcodes • Unique 20-mer tags (how many unique tags can you generate?) • 1.1 x 1012 How could you use these?

  8. What did this paper do? • Completed over 2000 of the mutants – why didn’t they finish them? • Now know there are 1063 essential genes in yeast • 8.5% of non-essential genes had a closely related gene in the genome (orthologs, paralogs)

  9. Genomic data is hard to present. Questions: Where are essential genes? What do essential and non-essential genes do?

  10. Highthroughput tests for viability. What mutants disappear from the population?

  11. Genomic analyses produce lots of maps like these:what genes were deleted

  12. Cited 459 times since Aug 1999

  13. Where to go with genomics papers • All of the reagents are likely to be available – you just need money to get them (usually) • What sorts of questions to ask? • How powerful is each technique/reagent?

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