Two resources that compile information from the many, many yeast expression microarray experiments that have been published:

SPELL (Serial Pattern of Expression Levels Locator): Looks for genes that are highly correlated in their expression patterns to the set of genes that you input as your search query. Delivers this nice graphical output showing the red-green “heat” map of the fold changes for each gene in each microarray experiment. On the other hand, my P.I. says that it’s prone to false positives: almost any set of genes you input will give you a result, regardless of whether it’s meaningful or not.

YFGdb (Yeast Functional Genomics Database): Has not only most of the .pcl files for the microarray experiments that are curated there, but also SGD Lite (a faster way to browse the yeast genome), Yeast SNP Genome Browser, and data for download.

Also, just for my own reference, here’s all the types of annotations given in SGD for yeast genome features:

• ARS
• binding site
• CDS
• chromosome
• centromere
• external transcribed spacer region
• five prime UTR intron
• gene
• gene cassette
• internal transcribed spacer region
• intron
• long terminal repeat
• LTR retrotransposon
• ncRNA
• noncoding exon
• nucleotide match
• pseudogene
• region
• repeat region
• rRNA
• snoRNA
• snRNA
• telomere
• transposable element gene
• tRNA