The microarrays were analyzed using

The microarrays were analyzed using the R program, version 2.15.1 (14), and the R package Piano (15) for microarray analysis. This package combines several other packages, as described below. The Affy package (16) was used to load the CEL files. Those were preprocessed using the Plier package (17) and applying cubic spline normalization. For further statistical pairwise analysis to determine significantly differentially expressed genes, the Limma package (18) was utilized for moderated Student's t test. The standard errors within each gene were moderated using empirical Bayesian statistics, and multiple testing was adjusted for by applying the Benjamini-Hochberg method (19). The P values and fold changes for each gene so obtained were further analyzed using the reporter algorithm (20) for gene ontology (GO) term analysis and reporter metabolites. For each gene set, distinct directional P values were calculated. The distinct directional P value is the outcome of two one-tailed t tests for either up- or downregulation, taking the transcriptional changes of all genes in the gene set into account. The case for the most significant distinct directional P value was chosen. Hence, the distinct directional P value, other than the directional P value, shows the overall significance of up- or downregulation of genes in a given gene set and not only the significance of the up- or downregulated genes
in the gene set. For the reporter metabolite analysis, the topology was inferred from the A. oryzae GEM. The topology for the GO term analysis was downloaded from the AspGD Aspergillus genome database (21).