Description of the general transcription response of spores to YPD medium. (a) The experimental design. Mature spores (prepared from strain DS1) were incubated in rich medium (YPD) to induce spore germination. Each circle represents a time point at which genome-wide gene expression was monitored; RNA was extracted, labeled and hybridized to a micorarray complementary to all (approximately 6,200) yeast ORFs. The reference RNA was a mixture of RNA from Mata and Matα log phase cells. (b) Rapid and intensive changes in gene expression - number of genes whose expression changed at least two-fold compared to the previous time point. To reduce noise, gene expression at each time point was the averaged expression in time points covering one hour, compared to a similar average during the previous hour, except for the first time point, which was compared to gene expression in spores. (c) Average expression of genes in specific modules  during spore germination. In parentheses is the number of genes in the module. Shown are log2 values of expression relative to expression in vegetative cells. See Additional data file 1 for a complete list of genes that are included in the different modules.