Fig. 3: Validation of candidate driver genes with concurrent copy number gain (CNG) and overexpression in TNBC cells.

a mRNA expression of 46 primary hits in 20 TNBC cell lines. Violin plot indicates Log2 mRNA expression level of 46 primary hits in 20 TNBC cell lines retrieved from RNA-Seq analysis. Bars indicate CNG frequency of the hits in 20 TNBC cell lines. Genes with frequent CNG in ≥8/20 TNBC cell lines were marked in red. b siRNA validation of primary candidate hits with high frequent CNG in BT549, Hs578T, and SUM149PT TNBC cell lines. SMARTpool siRNAs were used to target each hit. KIF11 was taken as positive control. c siRNA deconvolution validation of six candidate driver hits. The effects of SMARTpool (p) siRNA and single siRNA_1, _2, _3, and _4 on hits were compared for their proliferation control (%) in the TNBC cell lines. d Percentage of control proliferation (%) by optimized SMARTpool siRNAs targeting the six candidate hits. The results were expressed as mean ± SEM of three independent experiments. e CNA of the six candidate driver genes in TNBC cell panel. “++”, high CNG; “+”, CNG; “/”, no copy number alteration; “−”, copy number loss.