The Affymetrix 3' eukaryotic gene expression analysis arrays MOE430A_2 and HG-U133A were selected for this study. Probe sequence files and corresponding annotation files, 'Mouse430A_2_annot_csv.zip' (annotated on 2005-12-19) and 'HG-U133A_annot_csv.zip' (annotated on 2006-04-11), were downloaded from Affymetrix website [52] . Also downloaded there were the NetAffx probesetprotein mapping files for MOE430A_2 (file 'Mouse430A_2_blast_csv', updated on 2005-12-18) and HG-U133A ('HG-U133A.na21.blast.csv.zip', updated 2006-04-11), which were the blast results of the representative mRNA sequence of probes against protein sequence databases [26] . Ensembl transcripts: 37,854 mouse transcript sequences were obtained from the Ensembl database (release 38) [56] . Mapping tables between Ensembl Gene ID, Ensembl Transcript ID, and Ensembl Peptide ID were obtained from Ensembl martview [57] .