Table 2.

Features used for prediction in the optimal model and genes mapped to their respective genomic regions

RegionStart (Mb)End (Mb)Genes
Chromosomal gain7p11.254.757.1EGFR, ECOP, LANCL2, MRPS17, GBAS, PSPH, CCT6A, SUMF2, PHKG1, CHCHD2
11q13.369.570.1TMEM16A, FADD, PPFIAI, CTTN, SHANK2
17q1234.735.5FBXL20, CAB2, PPARBP, PPP1R1B, STARD3, TCAP, HER2 GRB7, ZPBP2, GSDML, PSMD3, CRK7, C17orf37
20q11.2232.933.3GGTL3, GSS, ACAS2, MYH7B, TRPC4AP, PROCR, C20orf44
20q13.251.651.8ZNF217
Chromosomal loss1p12119.9120TBX15, WARS2, HAO2, HSD3B1, HSD3B2, PHGDH
2q24.3166.4166.5GALNT3
9p24.199.1PTPRD
9p21.321.322.2IFNB1, IFNA7, IFNA5, KLHL9, IFNA13, IFNA1, CDKN2A, MTAP
  • NOTE: Genes in boldface were differentially expressed (P < 0.05), with fold change between sensitive and resistant cell lines concordant with that of DNA copy number.