To sum up, we re-annotated two popular Affymetrix gene expression arrays, MOE430_2 and HG-U133A, in a transcript-level perspective, aiming at identifying probesets' detecting targets precisely at the transcript level. Although previous works addressed similar issues [14, 15, 18, 19, 22, 23] , we are the first to rigorously link existing Affymetrix probesets to their specific transcript targets and their corresponding proteins. Armed with this new annotation, we re-examined a number of previous studies, 30 datasets for MOE430_2 and 28 datasets for HG-U133A from GEO, and revealed increased expression consistency among synonymous probesets and closer expression correlation among interacting proteins. This transcript-level annotation of Affymetrix probesets allows for a more reliable gene expression data analysis and a more accessible protein-level correlation study.