We downloaded 30 expression datasets assayed with MOE430A_2 from the Gene Expression Omnibus database (GEO) [24, 25] , and calculated the Pearson correlation coefficients (PCCs) of expression profiles of synonymous probesets at gene level and transcript level. Since transcript-level synonymous probesets in our work recognized a single protein-coding transcript variant identified with a unique IPI ID, transcript-level synonymous probesets were also named as protein-level synonymous ones. Practically, we grouped gene-level synonymous probesets according to gene ID, and protein-level ones according to IPI ID. The probeset-protein mapping tables provided at NetAffx, the official protein-level annotation of Affymetrix probesets [26] , was used as comparison. Probesets corresponding to a single protein according to NetAffx were designated as 'Affy-protein' level synonymous probesets, which was a third level of synonymy.