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

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

AgentInhibitor categoryGeneRegionCytobandNumber 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-263Bcl-2MDM2TSS20012q1570.52340.0617− 0.40170.0008− 0.42690.0004NM_002392 (MDM2)
ABT-737Bcl-2MDM2TSS20012q1570.52870.0617− 0.38670.0012− 0.42690.0004NM_002392 (MDM2)
BEZ-235mTORPTGFRNTSS15001p13.150.55650.0352*− 0.21890.0752− 0.47864.81 × 10−5NM_020440 (PTGFRN)
SapanisertibmTORIGFBP5TSS15002q3550.51070.08960.29690.01470.20350.1013NM_000599 (IGFBP5)
TAK-960PLK-1KDM1AGene body1p36.12110.54860.0352*− 0.23250.0583− 0.24360.0487NM_001009999 (KDM1A)
  1. 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. pFDR, p value adjusted for false discovery rate, accounting for multiple testing of 1376 candidate gene regions and 44 agents listed in Supplementary Table 2.
  2. *pFDR < 0.05
  3. ρ Spearman correlation coefficient, r Pearson correlation coefficient