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Table 2 Top 20 SFEs in terms of differential frequencies in pooled CIMP+ vs . pooled CIMP− samples

From: Pan-cancer stratification of solid human epithelial tumors and cancer cell lines reveals commonalities and tissue-specific features of the CpG island methylator phenotype

Selected functional event DifFreq Count CIMP+ Freq CIMP+ Count CIMP− Freq CIMP− P -value FDR
MLH1.METHYLATION 0.100 38 0.107 4 0.01 7.11 × 10 −13 3.40 × 10 −10
MGMT.METHYLATION 0.113 58 0.163 29 0.05 2.22 × 10 −08 5.30 × 10 −06
MFN1.PIK3CA.TERC.GNB4.SOX2.MECOM.ZMAT3.KCNMB3.ZNF639.KCNMB2..chr3.168753729.181290583_AMP −0.094 17 0.048 82 0.14 3.06 × 10 −06 4.89 × 10 −04
BRAF..BRAF_MUTATION 0.063 30 0.084 12 0.02 1.15 × 10 −05 1.38 × 10 −03
PTEN..PTEN_MUTATION 0.080 47 0.132 30 0.05 2.48 × 10 −05 2.38 × 10 −03
KRAS..KRAS_MUTATION 0.091 62 0.174 48 0.08 4.07 × 10 −05 3.25 × 10 −03
SETD2..SETD2_MUTATION 0.053 25 0.070 10 0.02 5.86 × 10 −05 4.01 × 10 −03
LOC148145.C19orf12.CCNE1..chr19.29379723.30313894_AMP −0.044 3 0.008 30 0.05 2.02 × 10 −04 1.21 × 10 −02
CACNA1A.BRD4.NOTCH3..chr19.15367544.15380857_AMP −0.035 1 0.003 22 0.04 2.98 × 10 −04 1.59 × 10 −02
PIK3R1..PIK3R1_MUTATION 0.046 25 0.070 14 0.02 1.10 × 10 −03 5.28 × 10 −02
DNM2..chr19.10877710.10887626_AMP −0.024 0 0.000 14 0.02 1.46 × 10 −03 6.35 × 10 −02
PBRM1..PBRM1_MUTATION 0.058 43 0.121 36 0.06 2.37 × 10 −03 9.46 × 10 −02
ATM..ATM_MUTATION 0.042 25 0.070 16 0.03 2.82 × 10−03 1.01 × 10−01
TP53..TP53_MUTATION −0.101 143 0.402 290 0.50 2.94 × 10−03 1.01 × 10−01
ARID1A..ARID1A_MUTATION 0.052 40 0.112 35 0.06 6.16 × 10−03 1.95 × 10−01
GSTP1.METHYLATION 0.054 44 0.124 40 0.07 6.51 × 10−03 1.95 × 10−01
SAMD4B..chr19.39837455.39850028_AMP −0.024 2 0.006 17 0.03 1.47 × 10−02 3.76 × 10−01
TMED11P.CTBP1.SPON2..chr4.1105313.1243877_DEL −0.016 0 0.000 9 0.02 1.55 × 10−02 3.76 × 10−01
KEAP1..KEAP1_MUTATION −0.016 0 0.000 9 0.02 1.55 × 10−02 3.76 × 10−01
FOSL2.PLB1..chr2.28628327.28860856_AMP −0.017 0 0.000 10 0.02 1.65 × 10−02 3.76 × 10−01
  1. Data included 356 CIMP+ samples and 577 CIMP− samples. P-values were computed using a two-sided Fisher’s exact test. SFEs with FDR < 0.10 are highlighted in bold font.
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Epigenetics & Chromatin

ISSN: 1756-8935