FIG. 6.

Benomyl treatment triggers a transcriptional response from genes involved in detoxification, cell cycle control, and the meiotic program. (A) Flow chart of the experimental protocol. Boxes indicate the samples analyzed in the results shown in Fig. 6 (see also Fig. S2 in the supplemental material). Box labels correspond to column labels in panels B and C. The flow chart also indicates the total time cultures spent in sporulation (SPO) medium. The time spent in SPO medium corresponds to the x axis of the graphs shown in panels D and E. (B and C) Loci involved in drug response and mitotic or meiotic cell cycles, as well as sporulation. The complete data set was analyzed using goCluster and split into 100 subgroups with similar expression using partitioning around medoids (26). The GO categories associated with the genes in each of the resulting groups were analyzed for statistically significant overrepresentation by comparing the frequencies of occurrence of the same GO term within the group and all transcripts represented on the microarray, respectively. The hypergeometric distribution was employed to determine the resulting P values (18). To correct for the multiple testing procedure, we used data from 100 randomized data sets to determine a P value cutoff that would result in a false discovery rate of 10%. A total of 586 different GO terms were identified as being enriched in one or several of the 100 clusters. Blue and red indicate low and high expression values, respectively. (D and E) Expression patterns of manually selected genes involved in drug response, cell cycle control and the regulation of mitotic and meiotic gene expression. Signals are given as log₂ transformed values on the y axis and are graphed versus the total time the cultures spent in SPO medium. Black arrows indicate the time of drug treatment or shift to low temperature. Note that low abundance mRNAs that are also cell cycle regulated (e.g., SWI4) are often not or only barely detectable in nonsynchronized heterogeneously growing cell populations.