Direct comparison of GeneChip and SAGE on the quantitative accuracy in transcript profiling analysis.

Among the high-throughput, comprehensive technological methods used to analyze transcript expression levels, array-based hybridization and serial analysis of gene expression (SAGE) are currently the most common approaches. To compare the quantitative accuracy of oligonucleotide array and SAGE, both methods were carried out on identical RNA specimens prepared from human blood monocytes and granulocyte-macrophage colony-stimulating factor (GM-CSF)-induced macrophages. For SAGE analysis, 57,560 and 57,463 tags were obtained from monocytes and macrophages, respectively, resulting in approximately 28,000 different tags, while oligo array hybridization was performed with GeneChip (Affymetrix), which represents approximately 6000 transcripts. These two methods correlated quite well in both absolute expression analyses and comparative analyses during differentiation. The correlation was better for genes with higher expression levels and greater changes in expression. This finding suggests that GeneChip technology is reasonably reliable for quantitative analysis of expression profiling and would be appropriate as a common platform upon which to build a gene expression database.