a For two major signaling pathways (PI3K-Atk and p53 pathways), the respective levels of activation and inactivation (red and blue, respectively) for 13 genes are shown. For each gene, activity levels are shown for benign CMTs, malignant CMTs, and human breast cancers, respectively. b CMT SCNAs are aligned onto the human reference genome (hg19) and compared with SCNA profiles of human breast cancers in the linear space of hg19 (chr1 to chr22 with sex chromosomes). The degrees of amplification and deletion are presented as the sum of log-ratios in hg19-aligned CMT and human breast cancer cohorts. c Chromosome 5 is shown, where human breast cancer shows arm-level 5p gains and 5q losses. The hg19-aligned CMT genomes show a deletion peak harboring PIK3R1. d Chromosome 8 shows peaks in six genes of hg19-aligned CMT SCNAs (CSMD, PSD3, IDO1, STK3, MYC, and PTK2), along with FGFR1 in an amplification peak of human breast cancer SCNAs.