Technology

Affymetrix GeneChip high-density oligonucleotide arrays (HDAs) were used in this study. The yeast genome HDAs are described in detail in ref. 20. The arrays can detect as few as 0.1 mRNA molecules/cell; the dynamic range over which detection is accurate is approximately 0.1 - 100 mRNA molecules/cell.

With the Genechip arrays, the entire yeast genome is covered by four HDAs. In total, 6181 ORFs are present within this set. Each gene is represented on the HDA by 20 25-mer oligos that match the sequence of the message (perfect match oligos) and 20 oligos that are identical but differ by one base (mismatch oligos). Expression levels are calculated by subtracting the signal of a mismatch from its perfect match partner and averaging the difference for each oligo pair for a given gene. The average difference value is a measure of the expression level of that gene. Based on various criteria (e.g. consistent behavior of each oligo pair) a Present or Absent call is also returned (more details at Affymetrix and ref. 20).