3.4. GSEA of DE genes by gcr2
DE genes in the gcr2 mutant were subjected to GSEA using Gene Ontology (GO) biological process (Table 4). On both glucose and xylose conditions, genes associated with translation, nucleotide biosynthesis, lipid biosynthesis, and one-carbon metabolism were up-regulated, and genes associated with protein transport were down-regulated. However, the direction of the transcriptional changes by gcr2 in two gene sets (sugar metabolism and oxidation-reduction) and their genes were opposites depending on the type of substrates; they were up-regulated on xylose but down-regulated on glucose (Fig. 3). For example, ALD3 , encoding aldehyde dehydrogenase, is known to be induced in response to stress; it was induced by gcr2 under xylose conditions but repressed under glucose conditions. Because Gcr2 is a native transcriptional activator for glucose metabolism, the heterologous xylose metabolism might interfere with the native metabolic regulation and cause some discrepancies in the direction of transcriptional regulation mediated by Gcr2.