Out of the total 22,690 and 22,283 probesets in arrays MOE430A_2 and HG-U133A, respectively, 64 and 68 control probesets were firstly removed. The remaining probesets were associated with genes according to the probeset-gene mapping information provided in Affymetrix's standard annotation file. The probeset-transcript mapping relationships were obtained based on the gene-mRNA mapping tables from GeneBank, RefSeq and Ensembl. In the process, we only included probesets that were identified with one Entrez Gene ID or one Ensembl gene ID. We ignored the probesets that were associated with multiple entities or no entity in the two gene-centric databases, since their gene-level specificity appears doubtful in the standard annotation file. This filtered out 3.2% and 5.2% of non-control probesets in MOE430A_2 and HG-U133A, respectively. For the rest of the probesets, we linked the candidate transcript targets to their corresponding protein entries in IPI database. IPI is currently the least redundant yet most complete protein database for featured species, with one protein sequence matching each transcript variant. Those probesets of which transcript tar-gets do not have any protein counterparts were also excluded from the following blast validation in order to focus our attention to the transcripts with well-characterized functions at protein level. The remaining probesets, 21,097 for MOE430A_2 and 16,213 for HG-U133A, were selected for the BLAST procedure.