1. Differential protein, mRNA, lncRNA and miRNA regulation by p53.
Differential protein, mRNA, lncRNA and miRNA regulation by p53. SW480/pRTR-p53-VSV were subjected to pSILAC, mRNA- and miRNA-Seq analyses after 48, 40 and 16 h DOX treatment, respectively. A, Volcano plot classification of proteins quantified in pSILAC experiments. Log-transformed p values (-log2) are plotted against the mean log2 of the corresponding pSILAC abundance ratios (induced/noninduced) of proteins quantified in at least two out of six replicates. Significantly regulated proteins with a log2 fold change ≥ 0.3 are indicated in green, with a log2 fold change ≤ -0.3 are marked in red and with 0.3 > log2 fold change > −0.3 in black. Proteins with a p value > 0.05 are represented by gray dots. B, C, rpkm scatter plot depicting expression changes of protein-coding mRNAs (B) and lncRNAs (C) detected by RNA-Seq. Transcripts with an rpkm < 0.5 in both conditions are shown in gray. Transcripts with a log2 fold change ≥ 1 are shown in green, with a log2 fold change ≤ −1 in red and with 1 > log2 fold change > −1 in black. D, Venn diagram displaying the overlap between quantified mRNAs (with an rpkm ≥ 0.5 in at least one condition) (shown in gray) and proteins (with a p value < 0.05) (shown in blue) and differentially regulated mRNAs (log2 fold change ≤ −1 or ≥ 1) (shown in orange) and proteins (log2 fold change ≤ −0.3 or ≥ 0.3) (shown in green). Genes differentially expressed on the mRNA level and the level of de novo protein synthesis are indicated in yellow. E, Cumulative distribution plot displaying changes in mRNA expression of up- and down-regulated proteins compared with the normal distribution of all mRNAs detected by RNA-Seq after activation of p53. F, Normalized read count scatter plot depicting expression changes of mature miRNAs. miRNAs with a log2 fold change ≥ 1 are shown in green, with a log2 fold change ≤ −1 in red and with 1 > log2 fold change > −1 in black.
Sabine Hünten et al. Mol Cell Proteomics 2015;14:
© 2015 by The American Society for Biochemistry and Molecular Biology, Inc.