Fig. 2
Description of top results for the RNA-Seq and MS3 proteomics experiments. Panels a and b display the distribution of log2 fold change values for the results with multiple comparison corrected significance obtained in proteomics (N = 283) and RNA-Seq (N = 1095) differential abundance analyses. The number of protein-coding genes assayed in the RNA-Seq experiment was almost five times larger than the number of proteins assayed in the MS3 proteomics experiment. Panel c summarizes the overlap between the genes analyzed by RNA-Seq and proteomics, either for all genes from the two experiments (upper part of panel c) or for the genes with multiple comparison corrected significance in one experiment and all genes from the other (lower part of panel c). The colors of the diagram sections indicate genes present only in the RNA-Seq experiment (blue), genes present in both the RNA-Seq and the proteomics experiments (green), and genes present only in the proteomics experiment (yellow). The brown boxes highlight the genes with multiple comparison corrected significance – either 1095 for RNA-Seq or 283 for proteomics. For the lower part of panel c, the green sections display two additional numbers (with percentages). These numbers represent the number of genes with multiple comparison corrected significance in one study and nominal significance in the other (first number), and the number of genes with multiple comparison corrected significance in one study, nominal significance in the other, and same direction of effect between the two studies (second number). Below the diagram corresponding to the “Intersection of Significant RNA-Seq and All Proteomics Genes” header, two additional percentages are displayed; they represent the percentages of genes with increased mRNA abundance in PD compared to control for the 1) 929 genes with multiple comparison corrected significance in the RNA-Seq study and not present in the proteomics study, and 2) 166 genes with multiple comparison corrected significance in the RNA-Seq study and present in the proteomics study (the two sections of the diagram directly above). Only 10 genes were in common between the RNA-Seq and proteomics results with multiple comparison corrected significance, with eight of them showing the same direction of effect and two of them (highlighted in red) showing opposite direction of effect, as displayed in panel d