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Table 1 Individual genes and genome regions containing multiple genes which contained methylation probes with the strongest Spearman correlations (p < 10−8) with log(IC50) of antitumor agents

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

AgentInhibitor categoryAssociated genesChromosomal locationHighest |ρ| for probe methylation vs log(IC50)Lowest p 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)
4SC-202HDACSNED12q37.30.69271.16 × 10−100.14920.22810.21780.0789NM_001080437 (SNED1)
BIM-46187Pan-G-proteinC8orf748p23.1− 0.67216.47 × 10−10     
R-547CDKTREX13p21.31− 0.66749.39 × 10−10     
CT-32228LPAAT-βSTK392q24.30.66201.43 × 10−9− 0.05750.6438− 0.17570.1581NM_013233 (STK39)
Pyrvinium pamoate FBXL187p22.10.66121.51 × 10−90.00830.9471− 0.04270.7333NM_024963 (FBXL18)
Digoxin KLHL2619p13.110.66061.58 × 10−90.02660.83090.26990.0284NM_018316 (KLHL26)
Astex FGF inhibitorFGFRTRIM24q31.30.65801.94 × 10−90.01430.9085− 0.15580.2117NM_015271 (TRIM2)
ENMD-2076Aurora kinaseNRP110p11.220.65662.14 × 10−90.12310.32120.39680.0010NM_003873 (NRP1)
OlaparibPARP1LHX41q25.20.65592.26 × 10−90.08030.51840.43030.0003NM_033343 (LHX4)
DepsipeptideHDACVWF12p13.31− 0.65352.70 × 10−9− 0.15860.19990.33110.0066NM_000552 (VWF)
TamoxifenSERMCABIN122q11.230.65103.26 × 10−9− 0.05750.6437− 0.23980.0525NM_012295 (CABIN1)
SNS-314Aurora kinaseTPM31q21.30.65073.34 × 10−90.16380.18540.07600.5441NM_152263 (TPM3)
ENMD-2076Aurora kinaseFOXN314q31.3− 0.65003.52 × 10−90.06380.6081− 0.05380.6677NM_001085471 (FOXN3)
DepsipeptideHDACFYN6q21− 0.64903.78 × 10−9− 0.11800.3415− 0.03570.7762NM_002037
(FYN)
XL-888HSP-90ETV6, RNU6-19P12p13.2− 0.64744.25 × 10−90.23870.0518− 0.28370.0210NM_001987 (ETV6)
DepsipeptideHDACMTERFD312q23.3− 0.64684.43 × 10−90.16860.1725− 0.31330.0104NM_001033050 (MTERFD3)
ARQ-197c-MetTRIM24q31.30.64984.73 × 10−9− 0.08010.5228− 0.15580.2117NM_015271 (TRIM2)
TAK-901Aurora kinaseTREX13p21.31− 0.64574.81 × 10−9     
FlavopiridolCDKATP13A33q29− 0.64345.68 × 10−90.17020.1685− 0.41600.0005NM_024524 (ATP13A3)
YK-4-279ERGTRIM24q31.30.64266.00 × 10−9− 0.10940.3782− 0.15580.2117NM_015271 (TRIM2 )
R-547CDKGIGYF22q37.10.64246.09 × 10−9− 0.12550.3114− 0.13500.2798NM_001103147 (GIGYF2)
R-547CDKSP217q21.320.64076.88 × 10−90.24840.04270.15290.2203NM_003110
(SP2)
ZIP-301 TRIM24q31.30.64066.93 × 10−9− 0.06690.5905− 0.15580.2117NM_015271 (TRIM2)
TAK-960 analogPLK-1FGF13Xq26.30.63967.42 × 10−9− 0.01330.91510.34070.0051NM_004114 (FGF13)
Digoxin SLC16A6, ARSG17q24.20.63897.83 × 10−9− 0.19180.1199− 0.30550.0126NM_014960 (ARSG)
SC-1Ras-GAPWT111p13− 0.63778.50 × 10−9− 0.32450.00740.52775.28 × 10-6NM_024424
(WT1)
DepsipeptideHDACAHSG3q27.3− 0.63748.66 × 10−9− 0.01010.93560.04290.7323NM_001622 (AHSG)
ONX-0912ProteasomeHRNBP317q25.3− 0.63689.06 × 10−9     
GSK-461364PLK-1NRP110p11.220.63679.09 × 10−90.25710.03570.39680.0010NM_003873 (NRP1)
SB-590885BRAFLOH12CR112p13.2− 0.63649.31 × 10−9− 0.18780.1280− 0.07110.5705NM_058169 (LOH12CR1)
FlavopiridolCDKCYP19A115q21.20.63609.54 × 10−90.16010.19550.14940.2313NM_031226 (CYP19A1)
  1. Shown are the strongest correlations with drug response, for genes or combined gene regions with at least one probe satisfying pO < 10−8 for Spearman correlation between methylation beta-values and log(IC50). Among multiple transcripts matching the same gene, the best matching transcript was identified by finding all Affymetrix transcripts with matching gene names and by selecting the most significant transcript from Spearman correlation between log2 of transcript expression and methylation of each probe within the gene/gene region that had been associated with log(IC50) of that agent with pO < 5 × 10−7. We also provide the NCBI or Ensembl ID of the transcript with a matching gene name that had the most significant Pearson correlation between log2 of transcript expression with log(IC50) of the agent. For those gene regions where probes with pO < 5 × 10−7 were assigned to multiple genes in the Infinium MethylationEPIC BeadChip manifest annotation [29] according to the UCSC genome annotation, the output summary for multiple genes was combined, as shown in the Gene Regions column for the regions combining ETV6 and RNU6-19P output and SLC16A6 and ARSG output. An expanded list of genes and combined genome regions containing multiple genes, each with at least one methylation probe satisfying pO < 9.42 × 10−8, is provided in Supplementary Table 4. Correlation results of log2 of expression of the most strongly correlated transcript with probe 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.
  2. Cluster ID transcript cluster ID for the Affymetrix GeneChip®Human Exon 1.0 ST Array, ρ Spearman correlation coefficient, r Pearson correlation coefficient, CDK cyclin-dependent kinase, HDAC histone deacetylase, LPAAT-β lysophosphatidic acid acyltransferase-β, PLK-1 polo-like kinase 1, SERM selective estrogen receptor modulator