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

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

• Winzeler, et al.

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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?

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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

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Genomics

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

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14 labs worked on this project
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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?

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Barcodes

• Unique 20-mer tags (how many unique tags can you
  generate?)

• 1.1 x 1012

How could you use these?
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What did this paper do?

• Completed over 2000 of the mutants why didnt
  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)

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Genomic data is hard to present. Questions
Where are essential genes? What do essential and
non-essential genes do?
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High throughput tests for viability. What
mutants disappear from the population?
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Genomic analyses produce lots of maps like
thesewhat genes were deleted
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Cited 459 times since Aug 1999
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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?