Figure 2

Correlation between protein and mRNA expression levels measured by Affymetrix arrays and RNA-Seq. Protein expression was measured in four individual samples with technical replicates. mRNA expression was measured by microarrays and RNA-Seq in two pooled samples (A, B, and E), and by microarrays in 5 individual samples (D). Shown are expression intensities of 520 (A and B) and 306 (D and E) genes expressed above background on all microarrays in a given experiment and represented by at least twenty independent sequence reads in RNA-Seq. (Cand F) Person correlation coefficients (r) from comparisons between RNA-Seq and protein measurements (blue) and between microarray and protein measurements (red) for two pooled samples and 5 individual samples, respectively. For RNA-Seq data, the correlations were based on each sequencing experiment separately and on average expression from all possible experiment combinations. For microarrays, the correlations were based on expression values from each microarray separately and on average expression from all possible microarray combinations (see Additional file 1: Table S4 for details).