FIG 3.

Graphic representation of differentially regulated proteins obtained by SILAC and RNA-Seq analyses. (a) Diagrams show the numbers of DE genes in RNA-Seq (left) and SILAC (right) results. Up- and downregulated factors were used separately for plotting. Numbers represent the factors with q values of <0.05 (RNA-Seq) or P values of <0.05 (SILAC). In bold, the numbers of factors with fold changes of at least ±1.5 (RNA-Seq) or ±1.3 (SILAC) are shown. For RNA-Seq results, numbers of DE genes shared by all four methods are shown in the center. (b) Heatmap of the 290 significantly altered proteins with at least a ±1.3 fold change from the corresponding genes in the RNA-Seq analysis using four bioinformatic workflows. One hundred fifty-five genes (upper part of heat map) displayed significant changes (q values of <0.05) in at least two of the four RNA-Seq data sets, whereas the other genes showed significant alterations in only one or none of the lists. (c) Graphic representation of the correlation of log₂ fold changes observed for factors from panel b between SILAC and RNA-Seq results. Values for RNA-Seq represent the averaged log₂ fold changes from all four lists. Blue and red dots show factors with q values of <0.05 in the RNA-Seq analysis that were significantly changed from values from the SILAC analysis. Gray dots show genes with q values of >0.05. Dashed lines represent cutoffs of ±1.5 fold change (RNA-Seq, x axis) or ±1.3 fold change (SILAC, y axis).