Figure 5

Comparison of protein copy numbers with mRNA levels and class-based analysis. (A,B) Protein copy numbers compared per gene to transcript levels (log2fpkm) for datasets of platelets (PLT, n = 3,519) (A) or megakaryocytes (MGK, n = 3,442). (B) Note triangular space, with low-abundance proteins (< 500 copies/platelet) were normalized to 150 copies. (C,D) Over-representation of protein function classes in quantitative proteome-transcriptome space per predefined area (I–V). Area I is considered to represent a condition of high translation (high mRNA level) and high transcription (high copy number); area II of high translation and low transcription; area III of low translation and transcription, and area IV an intermediate condition. Area V represents proteins without relevant transcript levels in PLT. Transcriptome-proteome triangle with analyzed areas (C). Enlarged space indicating function classes (C₀₁-C₂₁) with significant over-representation per area. Statistics in Suppl. Table 1.