Hierarchical clustering comparing the pattern of expression of Aspergillus niger grown on steam-exploded sugarcane bagasse (A). The color code displays the log2 ratio of cyanine 5 to cyanine 3 (Cy5/Cy3 ratio) for each time point with Cy3 used as the reference value (time point = 0, growth on fructose). The resulting significant data were visualized based on similar expression vectors using Euclidean distance and hierarchical clustering with an average linkage clustering method to view the whole data set. Clusters C1 to C3 and C4 to C6 show genes with decreased and increased mRNA accumulation, respectively, during growth of A. niger. Additional file 2, Table S2, and Additional file 3, Table S3, show genes that belong to these clusters. (B) and (C) The Functional Catalogue (FunCat) database http://mips.helmholtz-muenchen.de/proj/funcatDB/ functional annotation for the encoded proteins observed in clusters C1 to C6.