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Fig. 3 | BMC Medical Genomics

Fig. 3

From: Single-cell RNA sequencing reveals the impact of chromosomal instability on glioblastoma cancer stem cells

Fig. 3

Identification of copy number dependent and independent differentially expressed genes between CB660 NSCs and GliNS2 CSCs. a, Volcano plot showing both unadjusted and copy number adjusted differentially expressed genes between CB660 NSCs and GliNS2 CSCs. The dashed line shows the statistical significance cut-off (P.adjust< 0.05, Mann-Whitney U test and Bonferroni adjustment) used for differential gene expression analysis. Dark red points indicate genes that remain significantly differentially expressed after copy number adjustment while light red points indicate genes that are not significantly differentially expressed after copy number adjustment. b, Venn diagram showing the number of overlapping differentially expressed unadjusted and copy number adjusted genes. c, Scatter plot showing the correlation between the negative log10 transformed p-value of unadjusted and copy number adjusted differential gene expression analysis. Spearman correlation coefficient = 0.77. d, Scatter plot showing the correlation between c-MYC expression and c-MYC copy number in CB660 NSCs and GliNS2 CSCs. Spearman correlation coefficient = 0.54. e, Bar graphs quantifying c-MYC expression in CB660 NSCs and GliNS2 CSCs before (left graph) and after copy number adjustment (right graph). Bar, median; box 25th to 75th percentile; whiskers, minimum and maximum. P.adjust> 0.05 after copy number adjustment, Mann-Whitney U test and Bonferroni adjustment. f, Scatter plot showing the correlation between SLC23A2 expression and SLC23A2 copy number in CB660 NSCs and GliNS2 CSCs. Spearman correlation coefficient = 0.51. g, Bar graphs quantifying SLC23A2 expression in CB660 NSCs and GliNS2 CSCs before (left graph) and after copy number adjustment (right graph). Bar, median; box 25th to 75th percentile; whiskers, minimum and maximum. P.adjust = 4E-3 after copy number adjustment, Mann-Whitney U test and Bonferroni adjustment. h, Scatter plot showing the correlation between TFAP2C expression and TFAP2C copy number in CB660 NSCs and GliNS2 CSCs. Spearman correlation coefficient = − 0.02. i, Bar graphs quantifying TFAP2C expression in CB660 NSCs and GliNS2 CSCs before (left graph) and after copy number adjustment (right graph). Bar, median; box 25th to 75th percentile; whiskers, minimum and maximum. P.adjust = 0.02 after copy number adjustment, Mann-Whitney U test and Bonferroni adjustment

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