We tested whether integrative analysis was a reliable method to predict in vivo protein expression by analyses of two genes (BCL2L1 encoding an apoptosis regulator and CLDN1 encoding a component of tight junctions in epithelia) that showed a high frequency of copy number gains in HNSCC but were discordant with respect to correlation of copy number with gene expression in this study. Here, CLDN1 is linked to head and neck squamous cell carcinoma.