utilizing the Benjamini and Hochberg method in limma. Because specific genes were later validated by quantitative PCR (qPCR) and mutant analysis (see below), we did not use the fdr for further analysis (fdr values are included in Table S1). Genes with p < 0.05 difference in ethanol versus air exposure (1,807 genes) were clustered with the HOPACH algorithm (a bidirectional clustering method that maximizes cluster homogeneity; Salomonis et al., 2005). Gene ontology (GO) terms showing significant enrichment within each cluster were identified using the MAPPFinder algorithm in the GenMAPP package (http://www.genmapp.org). The microarray data have been deposited in NCBIs Gene Expression Omnibus and are accessible through GEO Series accession number GSE18208 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18208).
