Association of expression of epigenetic molecular factors with DNA methylation and sensitivity to chemotherapeutic agents in cancer cell lines

Table 1 Significant correlations of GMD expression with drug response in the pancancer dataset and in individual cancer categories satisfying |ρ| > 0.4 and p_FDR < 0.05

Cancer category	GMD	Agent	ρ	p_FDR	Sample size
Pancancer	KDM2B	XMD13-2	− 0.4319	3.99 × 10^–24	590
Pancancer	KDM2B	BMS-345541	− 0.4313	3.99 × 10^–24	590
Pancancer	KDM2B	T0901317	− 0.4231	3.83 × 10^–23	586
Pancancer	DNMT1	Zibotentan	− 0.4214	3.83 × 10^–23	591
Pancancer	KDM2B	NPK76-II-72–1	− 0.4174	1.01 × 10^–22	591
Pancancer	APOBEC3G	Z-LLNle-CHO	− 0.4148	2.64 × 10^–9	225
Pancancer	KDM2B	Zibotentan	− 0.4139	2.37 × 10^–22	591
Pancancer	KDM2B	Quizartinib	− 0.4095	8.98 × 10^–22	589
Pancancer	KDM2B	UNC1215	− 0.4062	5.08 × 10^–21	574
Pancancer	KDM2B	Daporinad	− 0.4057	7.77 × 10^–21	569
Pancancer	KDM2B	Vorinostat	− 0.4057	2.13 × 10^–19	527
Pancancer	DNMT1	XMD13-2	− 0.4043	2.87 × 10^–21	590
Pancancer	EHMT2	NPK76-II-72–1	− 0.4041	2.87 × 10^–21	591
Pancancer	DNMT1	Daporinad	− 0.4036	1.21 × 10^–20	569
Pancancer	KDM2B	XMD14-99	− 0.4035	3.24 × 10^–21	590
Pancancer	KDM2B	BX-912	− 0.4031	3.37 × 10^–21	590
Pancancer	KDM2B	I-BET-762	− 0.4020	5.08 × 10^–21	587
Pancancer	KDM2B	Tubastatin A	− 0.4011	5.97 × 10^–21	587
BREAST	GADD45A	Refametinib	− 0.8026	0.0002	40
MATBCL	BMI1	5-Fluorouracil	− 0.7900	0.0440	27
SCLC	APOBEC3A	GSK1070916	0.7764	0.0399	29
BREAST	APOBEC3C	Cetuximab	− 0.7278	0.0242	38
BREAST	APOBEC3G	Cetuximab	− 0.7105	0.0399	38
BREAST	GADD45A	Trametinib	− 0.7012	0.0399	39
NSCLC	IDH1	(5Z)-7-Oxozeaenol	0.5171	0.0242	91

All agents listed in table were from the GDSC dataset. Abbreviations for cancer categories are provided in Table S2 and in the list of abbreviations. ρ, Spearman correlation coefficient; p_FDR, FDR adjusted p-value; Sample size, the number of available cell lines in each category with available RNA-seq expression data and drug response data

ISSN: 1868-7083