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Table 1 Percentage of silent (SM) and truncating mutations (TM) affecting genes with different copy number alterations

From: Revealing selection in cancer using the predicted functional impact of cancer mutations. Application to nomination of cancer drivers

Cancer   Gene copy number alterations P-val (-1) P-val (+1)
   -1 0 1 2   
breast CNA: 13 64 21 2   
  SM: 12 65 22 2   
  TM: 17 64 18 2 <10-6 1.0E-06
lung CNA: 12 63 22 3   
  SM: 11 63 22 3   
  TM: 13 62 22 3 2.1E-05 3.9E-01
colon CNA: 12 71 17 1   
  SM: 11 71 17 1   
  TM: 14 72 14 1 1.1E-03 4.2E-04
brain CNA: 14 76 8 3   
  SM: 13 76 8 3   
  TM: 15 75 7 2 9.0E-06 4.9E-02
kidney CNA: 12 76 11 0   
  SM: 10 76 14 1   
  TM: 16 71 12 0 <10-6 1.2E-01
ovarian CNA: 23 51 24 2   
  SM: 21 53 24 2   
  TM: 30 49 19 2 <10-6 <10-6
  1. Silent mutations are distributed similar to distributions of CNA. Truncating mutations are distributed significantly differently as compared to silent mutations: over-presented in regions of heterozygous deletions; under-presented in regions of copy gains