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Table 1 Most frequently mutated or over/under-expressed chromatin factors in cancer

From: A global assessment of cancer genomic alterations in epigenetic mechanisms

Gene Cancer Mutated (%) q value Gene Cancer Overexpressed (%) Rank (out of 20,544) Gene Cancer Underexpressed (%) Rank (out of 20,544)
ATRX LGG 39.8 1.82E-11 HJURP PRAD 88 3 PRDM16 KIRP 100 14
ARID1A UCEC 32.3 8.11E-12 UHRF1 BRCA 94.7368 7 PRDM16 KIRC 95.8904 40
PBRM1 KIRC 28.5 1.76E-11 TDRD1 PRAD 84 14 KAT2B HNSC 82.9268 55
DNMT3A LAML 25.4 3.96E-12 DPF1 HNSC 87.8049 25 JMJD5 LIHC 88 56
MLL2 LUSC 19.1 6.39E-05 HJURP BRCA 91.2281 29 TDRD10 LUSC 100 57
ARID1A STAD 18.1 2.63E-11 HJURP LUAD 94.7368 31 MECOM KIRC 95.8904 62
MLL2 HNSC 17.7 1.94E-11 HJURP LIHC 96 34 L3MBTL4 PRAD 76 73
CHD4 UCEC 13.3 0.000958 ASF1B BRCA 91.2281 37 ASXL3 THCA 78.7879 81
STK31 SKCM 11.9 0.049702 UHRF1 KIRP 90 37 CECR2 THCA 80.303 83
NSD1 HNSC 10.8 1.89E-11 ORC1 LIHC 94 40 ZCWPW2 HNSC 80.4878 84
SETD2 KIRC 9.8 1.76E-11 EZH2 LIHC 94 44 ZGPAT LIHC 82 141
TET2 LAML 8.6 2.42E-11 ASF1B KIRP 90 45 TDRD10 BRCA 85.0877 154
EP300 HNSC 7.8 0.008196 HJURP LUSC 100 47 MECOM KIRP 93.3333 162
MLL3 BRCA 7.7 1.95E-11 UHRF1 LUSC 100 68 ACTA1 PRAD 70 194
SMARCA4 LUAD 7.4 2.99E-08 ORC1 LUAD 92.9825 72 CBX7 BRCA 83.3333 218
SETD2 LUAD 7 0.006858 ORC1 LUSC 100 79 TDRD9 THCA 71.2121 261
KDM5C KIRC 5.8 3.75E-11 ASF1B LUSC 100 90 TDRD6 BRCA 81.5789 277
ARID1A LUAD 5.7 0.001823 EZH2 LUSC 100 94 CHD5 PRAD 68 277
SMARCA4 LGG 4.5 0.035502 UHRF1 LUAD 89.4737 101 KIAA1045 BRCA 80.7018 298
KDM5C LUAD 4.4 0.091808 HIST1H3D BRCA 85.9649 102 CBX7 LUAD 85.9649 342
ARID1A BRCA 2.9 0.000117 TCF19 LIHC 88 102 SCML2 THCA 69.697 344
PHF6 LAML 2.5 0.001759 HJURP KIRP 83.3333 107 L3MBTL4 BRCA 79.8246 346
HIST1H1B HNSC 2.3 0.084637 CECR2 PRAD 72 107 DPF3 LIHC 72 364
HIST1H3B BRCA 1.1 9.81E-05 HIST1H3H BRCA 85.9649 109 CECR2 KIRC 83.5616 388
     UHRF1 LIHC 88 109 PRDM16 LUSC 92 410
  1. Values indicate the frequency of cancer patients where a gene is mutated (non-silent mutations only), where Log2(mRNA tumor/matched control) >1 for overexpression, or < -1 for underexpression. All data were extracted from TCGA and the ICGC. Patient cohorts are greater than 30 for overexpression and 100 for mutations. Hypermutated genomes and other sources of noise were excluded (as detailed in the Methods section). q value is a measure of the P value adjusted for false discovery rate. Ranks indicate the number of genes more frequently over- or underexpressed in the human genome.