Figure 3.

The expression responses of spores to YPD and glucose are qualitatively similar although YPD confer a stronger output than glucose. The gene expression program was compared between spores germinating in YPD and pure glucose media. (A) The number of core regulated genes changing at least two-fold up or down during the time course as positive and negative values, respectively. (B) The average fold change of the core regulated genes displayed as positive and negative values, respectively. (C) Two dimensional hierarchical clustering of the gene expression reprogramming during germination in YPD and glucose media. The x-axis represents the YPD cluster trees whereas the y-axis holds the glucose cluster trees. Three plots are separated by grey fields; genes two-fold changed in both the YPD and glucose data sets to the upper left, genes two-fold changed in glucose but not in YPD-induced germination to the upper right, genes two-fold changed in YPD but not in glucose induced germination to the lower left. Each cluster is subdivided into groups of genes with correlation factors ≥0.75 by thin black lines and the average expression profiles of groups of ≥ ten genes are framing the plots. The expression profiles of the genes that were up- or down regulated (≥two-fold) in glucose but not in YPD were heterogeneous in YPD (no clusters of ten or more genes with correlation factor ≥0.75) and are displayed in the upper right square. The colour panels along each axis indicates diminished expression of genes (blue) and stimulated genes (red), compared to dormant spores. Each gene occurs once on each axis and the number of genes (belonging to a cluster group of ≥10 genes with correlation factor ≥0.75) intersecting in each square is displayed. Also the genes in the upper right square are counted. The graphs displaying the average expression profiles are indexed with arabic and roman numerals for the YPD and glucose groups, respectively (error bars indicate standard deviation). The complete two dimensional hierarchical clustering with all genes included is depicted in Additional file 3. (D) The numerical summary of the two dimensional clustering, including all 1203 genes in the analysis, shows that the qualitative behaviour is very similar between the two germination conditions. However, as shown in (E), germination in glucose triggers a distinct subprogram encompassing genes in amino acid biosynthesis that is not induced in YPD,