-DNA microarray has been a useful tool for global-scale transcriptome analysis. To study the cellular response to expression of recombinant proteins, we compared the transcriptional profiles of recombinant Pichia pastoris strains overexpressing amylase and interleukin-2 versus that of the control strain at different cellular states. The microarray analysis was carried out via the use of Yeast_2 array specific for Saccharomyces cerevisiae and Schizosaccharomyces pombe. The transcirptome analysis of each studied strain at logarithmic growth phase and stationary growth phase showed hundreds of significant differences. In contrast, in comparison of studied strains at the same time points, the numbers of gene which are differentially expressed is rather low. Interestingly, the expression of heterologous alpha-factor secretion signal in the strains overexpressing amylase and interleukin-2 was up-regulated by more than 15 times and 140 times at the exponential and stationary phase, respectively. The results also provide evidence about the false positive result in microarray data when using non-specific array.