Epigenome-wide DNA methylation analysis of small cell lung cancer cell lines suggests potential chemotherapy targets

Table 4 Correlations in candidate gene regions with log(IC50) of candidate antitumor agents that satisfied p_FDR < 0.1

Agent	Inhibitor category	Gene	Region	Cytoband	Number of probes in gene region	ρ for average region methylation vs log(IC50)	p_FDR for average region methylation vs log(IC50)	Highest \|r\| for expression vs log(IC50)	Lowest p for expression vs log(IC50)	Highest \|ρ\| for expression vs region methylation	Lowest p for expression vs average region methylation	Transcript with lowest p for expression vs log(IC50)
ABT-263	Bcl-2	*MDM2*	TSS200	12q15	7	0.5234	0.0617	− 0.4017	0.0008	− 0.4269	0.0004	NM_002392 (MDM2)
ABT-737	Bcl-2	*MDM2*	TSS200	12q15	7	0.5287	0.0617	− 0.3867	0.0012	− 0.4269	0.0004	NM_002392 (MDM2)
BEZ-235	mTOR	*PTGFRN*	TSS1500	1p13.1	5	0.5565	0.0352*	− 0.2189	0.0752	− 0.4786	4.81 × 10⁻⁵	NM_020440 (PTGFRN)
Sapanisertib	mTOR	*IGFBP5*	TSS1500	2q35	5	0.5107	0.0896	0.2969	0.0147	0.2035	0.1013	NM_000599 (IGFBP5)
TAK-960	PLK-1	*KDM1A*	Gene body	1p36.12	11	0.5486	0.0352*	− 0.2325	0.0583	− 0.2436	0.0487	NM_001009999 (KDM1A)

Number of probes in gene region provides the number of probes annotated by the Illumina Infinium MethylationEPIC BeadChip manifest annotation [18] according to the UCSC genome browser as belonging to a particular gene region; methylation beta-values of all such probes were combined to compute the average region methylation value. Correlation results of log₂ of expression of the most strongly correlated transcript with gene region methylation and with log(IC50) are provided for those genes. p_FDR, p value adjusted for false discovery rate, accounting for multiple testing of 1376 candidate gene regions and 44 agents listed in Supplementary Table 2.
*p_FDR < 0.05
ρ Spearman correlation coefficient, r Pearson correlation coefficient

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