The analysis of gene differential expression is complicated by the potentially subtle differences associated with alterations in a single allele as well as by variations between individuals that arise from environmental or physiological factors. To circumvent these analytic problems, a method, named allele-specific differential expression analysis, was developed to compare the relative expression levels of two alleles of the same gene within the same cellular sample. The studies of allele-specific expression revealed that differential expression is relatively common in the human population.