Differential gene and pathway expression analysis of TP53 mutant compared with WT AMO-1 cells. (A) Principal-component analysis (PCA) projections of transcriptomes of AMO-1 (TP53 WT) and AMO-1–derived TP53 mutant cells (TP53 del/mut). The variability of the data set along principal component 1 (PC1) is 94% and along principal component 2 (PC2) is 4%. (B) Volcano plot indicating differentially expressed genes in TP53 mutant relative to TP53 WT AMO-1 cells. 499 significantly downregulated genes are shown in blue and 393 significantly upregulated genes in red (cutoff: log2 fold change of 1 and .05 adjusted P value). (C) Analysis of TP53 messenger RNA expression levels (transcripts per million [TPM]) shows similar expression values in AMO-1 (TP53 WT) and AMO-1–derived TP53 mutant cells (TP53 del/mut). (D) Gene set enrichment analysis (GSEA) of KEGG pathways (MsigDB) significantly regulated in TP53 mutant relative to TP53 WT AMO-1 cells. For all pathways shown, a false discovery rate q-value of <0.25 was chosen as cutoff for exploratory data analysis. (E) Gene set enrichment analysis enrichment plot for the p53 signaling pathway (KEGG) indicates a downregulation in TP53 mutant cells. (F) Bar plot for all differentially expressed genes of the p53 signaling pathway (KEGG). Log2 fold changes of genes downregulated in TP53 mutant cells are shown in blue and upregulated genes in red. Error bars indicate the standard error estimate for the log2 fold change in TP53 mutant relative to TP53 WT AMO-1 cells.