Two Affymetrix arrays, MOE430A_2 and HG-U133A, were chosen for this study, in which 21,097 and 16,213 putative protein-coding probesets for the two arrays were subject to the alignment investigation (Table 1) . Candidate probeset-mRNA relationships were compiled based on the probeset-gene mapping information specified in the standard Affymetrix annotation files and gene-mRNA mapping relationships provided by separate mRNA transcript sources. Rigorous blast procedure similar to that described in [22] were performed to filter these candidate probeset-mRNA relationships. Finally, the mRNA targets passing the filtering criteria were linked to protein IDs in the IPI database.