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Table 3 Candidate genes with methylation probes that had correlations with log(IC50) of candidate antitumor agents satisfying pFDR < 0.1

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

AgentInhibitor categoryAssociated geneLocationHighest |ρ| for probe methylation vs log(IC50)Lowest pFDR for probe methylation vs log(IC50)Highest |r| for transcript expression vs log(IC50)Lowest p for transcript expression vs logIC50Highest |ρ| for transcript expression vs probe methylationLowest p for transcript expression vs probe methylationTranscript with lowest p for expression vs log(IC50)
ABT-348Aurora kinaseEPAS12p210.55480.05150.36380.00250.68003.39 × 10−10NM_001430 (EPAS1)
ABT-737Bcl-2DLL319q13.20.55060.0515− 0.41390.0005− 0.44260.0002NM_016941 (DLL3)
ABT-737Bcl-2FHIT3p14.2− 0.55020.05150.18300.1382− 0.31640.0097ENST00000468189 (FHIT)
ABT-737Bcl-2KIT4q12− 0.53910.0580− 0.53722.77 × 10−60.54262.52 × 10−6NM_000222 (KIT)
ABT-737Bcl-2EPAS12p21− 0.52040.0937− 0.05010.68730.26380.0324NM_001430 (EPAS1)
AMG-900Aurora kinaseEPAS12p210.62780.0052*0.39660.00090.68003.39 × 10−10NM_001430 (EPAS1)
AS-703569Aurora kinaseCCND111q13.3− 0.55680.0515− 0.36140.00270.59721.20 × 10−7NM_053056 (CCND1)
BEZ-235mTORAKT114q32.33− 0.53700.06040.25620.0363− 0.34990.0040NM_001014432 (AKT1)
BI-2536PLK-1KIF249p13.30.54030.05800.17400.15910.06890.5828NM_194313 (KIF24)
CYC-116Aurora kinaseEZH27q36.10.54560.0515− 0.01620.8966− 0.11560.3554NM_004456 (EZH2)
ENMD-2076Aurora kinaseCCND111q13.3− 0.57770.0391*− 0.42010.00040.59721.20 × 10−7NM_053056 (CCND1)
ENMD-2076Aurora kinaseALK2p23.2− 0.55510.05150.00360.97680.23310.0597NM_004304 (ALK)
ENMD-2076Aurora kinaseEPHA21p36.130.52330.0876− 0.20900.0897− 0.37870.0017NM_004431 (EPHA2)
ENMD-2076Aurora kinaseRGS71q430.51910.09480.48872.72 × 10−50.74121.11 × 10−12NM_002924 (RGS7)
GSK-461364PLK-1EPAS12p210.51650.09940.35540.00320.68003.39 × 10−10NM_001430 (EPAS1)
SapanisertibmTORIGF1R15q26.30.52620.0798− 0.08890.4744− 0.13690.2730NM_000875 (IGF1R)
MLN-8237Aurora kinaseEPAS12p210.54620.05150.32450.00740.68003.39 × 10−10NM_001430 (EPAS1)
OlaparibPARP1SEMA3B3p21.310.52640.0798− 0.08150.51200.09070.4687NM_004636 (SEMA3B)
SNS-314Aurora kinaseEPAS12p210.58800.0322*0.34340.00440.68003.39 × 10−10NM_001430 (EPAS1)
SNS-314Aurora kinaseEZH27q36.10.54640.0515− 0.04440.7215− 0.11560.3554NM_004456 (EZH2)
TAK-901Aurora kinaseZNF42316q12.1− 0.53600.0604− 0.18590.13190.57733.88 × 10−7NM_015069 (ZNF423)
TAK-960PLK-1KIF249p13.30.55710.05150.22850.06300.06890.5828NM_194313 (KIF24)
TAK-960PLK-1MYC8q24.210.54320.0540− 0.15370.21430.26520.0314NM_002467 (MYC)
SalinomycinApoptoticFGFR210q26.13− 0.53340.0650− 0.32370.00750.67853.84 × 10−10NM_000141 (FGFR2)
SalinomycinApoptoticKIF3B20q11.21− 0.52020.09370.19380.1162− 0.45760.0001NM_004798 (KIF3B)
  1. Listed are the gene-drug correlations for candidate genes in which one or more probes had pFDR < 0.1 for Spearman correlation with agents listed in Supplementary Table 2. Supplementary Table 6 provides the list of candidate gene-drug pairs satisfying a less stringent criterion of pFDR < 0.15. The list of individual probes and their individual p values are provided in Supplementary Table 7
  2. pFDR, FDR-adjusted p value, accounting for multiple testing of 10,515 methylation probes in or near candidate genes and 44 agents listed in Supplementary Table 2.
  3. *pFDR < 0.05
  4. ρ Spearman correlation coefficient, r Pearson correlation coefficient