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Table 2 Gene regions with FDR-adjusted p value for Spearman correlations of average gene region methylation with log(IC50) of antitumor agents < 0.1

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

AgentInhibitor categoryAssociated geneGene regionCytobandNumber of probes in gene regionρ for average region methylation vs log(IC50)pFDR 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 methylationLowest p for expression vs average region methylationTranscript with lowest p for expression vs log(IC50)
ABT-348Aurora kinaseCEP350UTR31q25.210.60960.09530.02700.8281− 0.18870.1292NM_014810 (CEP350)
ABT-737Bcl-2TCERG1LUTR310q26.36− 0.62510.0787− 0.57403.81 × 10−70.60268.64 × 10−8NM_174937 (TCERG1L)
AZD-1152Aurora kinaseMLPHUTR32q37.310.61480.09050.30140.01320.53962.94 × 10-6NM_024101 (MLPH)
BAL-101553Tubulin fragmenterSTARD3UTR317q1250.61540.09050.07540.5440− 0.01730.8900NM_006804 (STARD3)
BI-2536PLK-1MLPHUTR32q37.310.61720.09050.24860.04250.53962.94 × 10-6NM_024101 (MLPH)
BIAGSK-3TTC15TSS2002p25.340.61380.0905− 0.11910.3372− 0.16680.1807NM_016030 (TTC15)
BIM-46187Pan-G-proteinC8orf74UTR58p23.11− 0.67210.0145*     
BIM-46187Pan-G-proteinC8orf74Exon 18p23.11− 0.67210.0145*     
BIM-46187Pan-G-proteinC8orf74TSS2008p23.13− 0.64590.0530     
DepsipeptideHDACMTERFD3Gene body12q23.31− 0.64680.05300.16860.1725− 0.31330.0104NM_001033050 (MTERFD3)
FlavopiridolCDKSEC11CTSS150018q21.3240.61800.09050.07310.55660.54761.95 × 10-6NM_033280 (SEC11C)
GSK-461364PLK-1LOC100128568Gene body19p13.3200.62670.0787     
SapanisertibmTORSPG20UTR513q13.3280.62520.0787− 0.31220.0101− 0.54232.55 × 10−6NM_001142295 (SPG20)
Ivacaftor MIFTSS20022q11.2360.61440.0905− 0.26850.0280− 0.43180.0003NM_002415 (MIF)
Ivacaftor RPUSD2Exon 115q15.140.61270.0913− 0.07290.5575− 0.09080.4683NM_152260 (RPUSD2)
ONX-0912ProteasomeCYP11B2Gene body8q24.31− 0.60780.0992− 0.14140.25360.17050.1711NM_000498 (CYP11B2)
R-547CDKGIGYF2TSS15002q37.140.63540.0639− 0.12550.3114− 0.15250.2215NM_001103147 (GIGYF2)
R-547CDKKCNH6UTR517q23.340.64090.06070.06770.58610.16640.1818NM_030779 (KCNH6)
R-547CDKTREX1Exon 13p21.319− 0.61190.0913     
R-547CDKTREX1UTR53p21.316− 0.61090.0913     
SC-1Ras-GAPWT1UTR311p131− 0.63720.0639− 0.32450.00740.40040.0009NM_024424 (WT1)
SCH-1473759Aurora kinaseITPAUTR320p131− 0.61100.09130.01380.9115− 0.05620.6537NM_033453 (ITPA)
SNS-314Aurora kinaseCEP350UTR31q25.210.62800.0787− 0.07040.5713− 0.18870.1292NM_014810 (CEP350)
TAK-901Aurora kinaseTREX1Exon 13p21.319− 0.62310.0796     
TAK-901Aurora kinaseTREX1UTR53p21.316− 0.60880.0969     
TAK-960 analogPLK-1GLYATL1TSS150011q12.120.61640.09050.12280.32230.43040.0003NM_080661 (GLYATL1)
Vertex ATR inhibitor Cpd 45ATRTREX1Exon 13p21.319− 0.62440.0787     
Vertex ATR inhibitor Cpd 45ATRTREX1UTR53p21.316− 0.61820.0905     
  1. 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 that had matching transcript data in the Affymetrix GeneChip®Human Exon 1.0 ST Array. 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. pFDR p value adjusted for false discovery rate, accounting for all 412 drug agents with variable drug response and 108,795 gene regions
  2. *pFDR < 0.05
  3. ρ Spearman correlation coefficient, r Pearson correlation coefficient, ATR ataxia telangiectasia and Rad3-related protein, CDK cyclin-dependent kinase, GSK-3 glycogen synthase kinase 3, PLK-1 polo-like kinase 1