CSE 527 Lecture 3, Monday 10/06/03
Microarrays, II

Notes by Tin L. Louie <tinlouie@u.washington.edu>

Sources of noise in the data include:

• lot -- differences in chips, differences in reagents used
• experiment -- purity of the cell culture, hybridization conditions
• spot -- self-hybridization (think hairpin loops)
              cross-hybridization
              dye bias (different sequences have different hybridization efficiencies)
              dye saturation (nonlinear response, plateau)

(most of the following notes were taken by Autumn 2001 student Simon Kahan:)
Case Study: The Transcriptional Program of Sporulation in Budding Yeast (Science, Vol 282, October 1998, Chu et al.)

Meiosis is typically described as being divided into four phases: early, middle, mid-late, and late corresponding to replication/recombination, meiosis I, meiosis II, and spore maturation.

Transcription in the early and middle phases has been studied in experiments predating this paper.
150 genes had been implicated in the sporulation process, via laborious knockout experiments.

In this work, the authors compare the levels of mRNA present over time using a series of microarrays. They found 500 genes that are induced/up-regulated and 500 that are repressed/down-regulated.

The pattern of expression as assayed by (traditional) Northern analysis was very similar to that determined by microarray analysis

Clustering the microarray data suggests division into seven temporal profiles rather than four phases: a refinement of the earlier sporulation process description.

More in the next lecture ...