Supplement Table 1. Categorization of 318 cancer cell lines and the occurrence of category-sensitive (and specific) gene expression markers. Lineage and the existence of particular mutations are used for the categorization. The criteria for the sensitive transcript marker is >2-fold change of gene expression (p<0.01) over median value. The criteria for the specific transcript marker is enrichment score (ES score) of > 1 (fisher p<0.01) in the given category. Each category includes at least 3 cell lines.

Lineage / # of cell lines / # of transcript markers
Sensitive / Sensitive and specific
Leukemia/Lymphoma / 56 / 840 / 347
Skin / 12 / 414 / 91
Colon / 23 / 316 / 63
Breast / 19 / 281 / 61
Liver / 9 / 300 / 27
Renal / 8 / 279 / 25
Sarcoma / 19 / 249 / 24
Pancreatic / 9 / 374 / 24
CNS / 11 / 228 / 17
Lung / 76 / 78 / 14
Cervical / 7 / 131 / 9
urinary tract / 9 / 82 / 6
Stomach / 5 / 130 / 3
Ovarian / 5 / 30 / 1
Esophagus / 4 / 80 / 10
Autonomic Ganglia / 4 / 125 / 8
Thyroid / 4 / 55 / 6
Endometrial / 4 / 49 / 3
Prostate / 4 / 14 / 0
Single mutation / # of cell lines / # of transcript markers
Sensitive / Sensitive and specific
RB1 / 31 / 221 / 44
APC / 17 / 233 / 32
STK11 / 17 / 145 / 19
BRAF / 29 / 72 / 10
PIK3CA / 34 / 42 / 4
KRAS / 60 / 41 / 2
MYC-Amp / 23 / 37 / 1
NRAS / 21 / 25 / 1
CDKN2A / 101 / 21 / 1
PTEN / 38 / 38 / 0
CTNNB1 / 30 / 21 / 0
TP53 / 158 / 9 / 0
Combination of two mutation / # of cell lines / # of transcript markers
Sensitive / Sensitive and specific
RB1 and TP53 / 26 / 188 / 33
BRAF w/o TP53 / 17 / 164 / 27
APC and TP53 / 15 / 230 / 26
STK11 and TP53 / 12 / 157 / 15
PTEN w/o TP53 / 10 / 172 / 12
RB1 w/o TP53 / 5 / 114 / 6
STK11 w/o TP53 / 5 / 58 / 3
CDKN2A w/o TP53 / 44 / 51 / 3
KRAS and TP53 / 41 / 38 / 3
MYC-Amp w/o TP53 / 10 / 84 / 2
PIK3CA and TP53 / 24 / 39 / 2
CTNNB1 and TP53 / 11 / 40 / 1
NRAS w/o TP53 / 11 / 32 / 1
MYC-Amp and TP53 / 13 / 31 / 1
PIK3CA w/o TP53 / 10 / 32 / 0
NRAS and TP53 / 10 / 22 / 0
CTNNB1 w/o TP53 / 19 / 31 / 0
KRAS w/o TP53 / 19 / 34 / 0
BRAF and TP53 / 12 / 16 / 0
PTEN and TP53 / 28 / 22 / 0
CDKN2A and TP53 / 57 / 19 / 0
APC w/o TP53 / 2 / 0 / 0
Combination of mutation and lineage / # of cell lines / # of transcript markers
Sensitive / Sensitive and specific
TP53 and Leukemia/Lymphoma / 28 / 825 / 246
RB1 and Lung / 20 / 766 / 204
KRAS and Colon / 13 / 411 / 80
CDKN2A and Leukemia/Lymphoma / 18 / 579 / 79
APC and Colon / 12 / 451 / 74
BRAF and Skin / 8 / 472 / 71
PIK3CA and Breast / 11 / 351 / 62
TP53 and Colon / 14 / 341 / 56
CDKN2A and Skin / 8 / 380 / 56
PTEN and Leukemia/Lymphoma / 8 / 594 / 47
PTEN and Skin / 4 / 336 / 41
CDKN2A and Liver / 4 / 296 / 41
TP53 and Lung / 58 / 133 / 35
STK11 and Lung / 13 / 261 / 32
TP53 and Breast / 12 / 256 / 31
PTEN and Lung / 7 / 376 / 31
KRAS and Leukemia/Lymphoma / 6 / 381 / 23
PIK3CA and Colon / 6 / 246 / 21
PTEN and CNS / 7 / 275 / 20
CDKN2A and Renal / 6 / 290 / 20
CTNNB1 and Liver / 6 / 218 / 15
TP53 and Pancreatic / 5 / 229 / 15
CDKN2A and Lung / 26 / 121 / 14
KRAS and Pancreatic / 8 / 310 / 14
CDKN2A and Pancreatic / 8 / 310 / 14
NRAS and Leukemia/Lymphoma / 8 / 307 / 13
CDKN2A and Breast / 7 / 180 / 13
CDKN2A and CNS / 6 / 230 / 12
CTNNB1 and Colon / 5 / 220 / 9
CTNNB1 and Breast / 6 / 93 / 8
PTEN and Breast / 4 / 50 / 8
NRAS and Liver / 3 / 46 / 8
TP53 and Thyroid / 3 / 27 / 6
MYC-Amp and Autonomic Ganglia / 3 / 36 / 5
KRAS and Lung / 19 / 46 / 4
CTNNB1 and Lung / 6 / 75 / 3
MYC-Amp and Leukemia/Lymphoma / 4 / 169 / 3
BRAF and Sarcoma / 4 / 67 / 3
TP53 and Sarcoma / 8 / 131 / 2
CDKN2A and Sarcoma / 7 / 123 / 2
MYC-Amp and Lung / 6 / 42 / 2
BRAF and Breast / 4 / 52 / 2
TP53 and Liver / 3 / 38 / 2
TP53 and urinary tract / 7 / 32 / 1
BRAF and Colon / 5 / 84 / 1
RB1 and urinary tract / 5 / 34 / 1
TP53 and CNS / 4 / 87 / 1
PIK3CA and
urinary tract / 4 / 18 / 1
BRAF and Lung / 3 / 30 / 1
TP53 and Endometrial / 3 / 16 / 1
PTEN and urinary tract / 3 / 4 / 1
PIK3CA and Lung / 5 / 12 / 0
KRAS and Breast / 4 / 28 / 0
MYC-Amp and Colon / 4 / 25 / 0
CDKN2A and
urinary tract / 4 / 9 / 0