Fig. 1: Featured ACGEJ genomic and transcriptomic changes.

a Frequencies of CNVs detected in 124 ACGEJ samples, with gains in red and losses in blue. Bars represent non-overlapped 1-million-base-pair windows along the genome. b Bar plot comparing the number of genes altered by CNVs and SNVs/indels in each of 120 ACGEJ genomes with both types of alterations. The y-axis indicates the ratio of CNVs to SNVs/indels minus 1. Only deletions, amplifications, or non-silent coding mutations are counted. Most samples (102/120, 85%) show a preponderance of CNVs over SNVs/indels. c GSEA analysis comparing CIN70 activities in ACGEJ samples and adjacent normal tissue samples. The plot shows overexpressed CIN70 in ACGEJ samples, the normalized enrichment score (NES) and the P value. d Associations between CIN70 activities and the WGD status (+ and − indicating 74 and 50 tumor genomes with and without WGD, respectively; two-sided Wilcoxon rank-sum test), the number of chromosomal (Chr.) arm or gene level CNVs (Spearman’s correlation tests) in ACGEJ samples. e GISTIC2.0 identified recurrent focal CNVs in 124 ACGEJ genomes, with 25 potential CNV drivers annotated on the plot. f Box and bar plots comparing chromosomal (Chr.) arm level CNVs, gene level CNVs, and the frequencies of WGD in tumor genomes with and without CCNE1 copy number gains (n = 67 and 57, respectively; two-sided Wilcoxon rank-sum tests). g Associations between CCNE1 expression levels and CIN70 activities (Spearman’s correlation test) or WGD status (two-sided Wilcoxon rank-sum test) in ACGEJ samples. Box plots in (d, f, g) show the median (central line), the 25–75% interquartile range (IQR) (box limits), the ±1.5 times IQR (Tukey whiskers), and all data points, among which the lowest and the highest points indicate minimal and maximal values, respectively.