Fig. 2.

MALAT1 knockdown induced perturbation of gene expression at the transcriptome and proteome level.A, the relative expression of MALAT1 in the negative control (siNC) and siMALAT1-treated HCCLM3 cells as measured by qRT-PCR. Data represent mean ± s. d. of triplicate independent experiments (∗∗∗p < 0.001, by two-sided Student’s t test). B, the overlap of genes quantified at the RNA and protein levels. C, percentages of the indicated biotypes of the quantified transcripts. D, comparison of the protein intensities as in intensity-based absolute quantification (iBAQ) values versus mRNA intensities (TPM). Pearson correlation analysis was conducted. E and H, the percentages of the differently expressed transcripts (E) and proteins (H). F and I, volcano plots and heatmaps showing the differently expressed transcripts (F) and proteins (I). G and J, principal component analysis of all quantified RNAs (G) and proteins (J).