Cross-sections, profiles and overrepresented functional categories of the pair-wise comparisons. Transcript data from independent chemostat cultures of P. chrysogenum strains DS17690 and DS50661 grown at D = 0.03 h-1 in the presence and absence of phenylacetic acid (PAA) were compared in four pairwise comparisons (DS17690 + PAA versus DS17690 - PAA; DS50661 + PAA versus DS50661 - PAA; DS17690 + PAA versus DS50661 + PAA and DS17690 - PAA versus DS50661 - PAA. Genes whose transcript level was significantly different in at least one of the four pairwise comparisons were overlapped as shown in A, resulting in 12 different groups of genes: 1–6: compare the response to PAA in DS17690 and DS50661; 7–12 compare the effect of the cluster removal. B shows the gene-transcript profiles of the groups of specific interest with the results of the hypergeometric distribution analysis for enrichment of functional categories. The thick line represents the average of the mean normalized transcript data of the genes comprising the cluster. The y-axis represents 10log transcript values. Functional categories are mentioned together with their P-value and the number of genes in the respective functional category in the group of genes with a higher transcript level compared to the prevalence of this functional category in the whole genome. Due to a large redundancy in the functional categories some categories might appear without having a significant biological relevance.