Often changes in gene expression levels have been considered significant only when above/below some arbitrarily chosen threshold. We investigated the effect of applying a purely statistical approach to microarray analysis and demonstrated that small changes in gene expression have biological significance. Whole genome microarray analysis of a pde2⌬ mutant, constructed in the Saccharomyces cerevisiae reference strain FY23, revealed altered expression of ϳ11% of protein encoding genes. The mutant, characterized by constitutive activation of the Ras/cAMP pathway, has increased sensitivity to stress, reduced ability to assimilate nonfermentable carbon sources, and some cell wall integrity defects. Applying the Munich Information Centre for Protein Sequences (MIPS) functional categories revealed increased expression of genes related to ribosome biogenesis and downregulation of genes in the cell rescue, defense, cell death and aging category, suggesting a decreased response to stress conditions. A reduced level of gene expression in the unfolded protein response pathway (UPR) was observed. Cell wall genes whose expression was affected by this mutation were also identified. Several of the cAMP-responsive orphan genes, upon further investigation, revealed cell wall functions; others had previously unidentified phenotypes assigned to them. This investigation provides a statistical global transcriptome analysis of the cellular response to constitutive activation of the Ras/cAMP pathway. constitutive activation of PKA by PDE2 deletion; Ras/cAMP pathway; cell wall integrity THE RAS/CAMP PATHWAY is a highly conserved signal transduction pathway operating via the second messenger, cAMP (6). In Saccharomyces cerevisiae, it controls cell-cycle progression, cell growth and proliferation (3, 81), reprogramming of transcription at the diauxic transition (8), mating (1), pseudohyphal morphogenesis (27, 55), metabolism (9), and stress responses. The synthesis of cAMP is catalyzed by adenylate cyclase (40), which is regulated by Ras proteins (18,24,80), the G protein ␣-subunit homolog, Gpa2 (48), and the adenylate-cyclase-associated protein, Cap1p (23,25). The only known biochemical role of cAMP is to activate protein kinase A (PKA) (12,78,79). High activity of PKA in yeast leads to low levels of the storage carbohydrates trehalose and glycogen, low stress resistance due to reduced expression of STRE ("stress response element")-controlled genes, aberrant G 0 arrest, poor growth on nonfermentable and weakly fermentable carbon sources, and failure of sporulation in diploid cells. Low activity yields de-repression of STRE-controlled genes leading to high stress resistance, constitutive expression of heat-shock genes, and sporulation of diploid cells in rich media (for reviews, see Refs. 10,64,[74][75][76]. Two trans-acting factors (Msn2p and Msn4p), negatively regulated by PKA, have been shown to be involved in STRE-mediated gene expression (47,67).Intracellular levels of cAMP, and hence the state of the Ras/cAMP pathway, are also contr...