Fig 2. Principal component analysis (PCA), correlation analysis and MA plot of differential gene expression data.

(A) PCA plot of log2 gene expression data showing the 2^nd and 3^rd principal components. (B) Heatmap visualization of the Pearson correlation coefficients of log₂ gene expression between samples. The three samples from wild type KBM-7 cells are labeled WT1-WT3 and those from the KBM-7-NuKO cells KO1-KO3. (C) MA plot showing the distribution of mean gene expression levels (log₂Counts Per Million mapped reads) against log₂ Fold-Change (KO vs WT) for individual gene responses. Low expression genes (log₂CPM < −5) are colored orange. Significant differentially expressed genes (DEGs) are colored red; genes showing no change in expression are colored black.