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Table 3 Comparing the performances of the integrative approach and the Cancer Linker Degree method. Positive predictive values (PPV) and sensitivities are shown under nine different fixed cancer linker degrees (CLD) for a method solely based on CLD scores and an integrative approach which combines the CLD score with SF-Probability and the number of cancer types in which the gene appears differentially expressed. For all CLD thresholds above 3, the difference between the integrative approach and the CLD method alone is not significant. The p-value of the difference between the two different groups of cancer gene candidates was calculated using the Fisher's exact test.

From: Predicting cancer involvement of genes from heterogeneous data

  CLD alone Integrative approach • SF-Probability ≥ 0.3 • No. Cancer types ≥ 1 P-value
  PPV Sensitivity PPV Sensitivity  
CLD ≥ 1 15% 67% 26% 11% 4.2 × 10-9
CLD ≥ 2 21% 53% 28% 9% 0.005
CLD ≥ 3 26% 44% 32% 8% 0.035
CLD ≥ 4 30% 36% 34% 6% 0.194
CLD ≥ 5 34% 30% 39% 6% 0.245
CLD ≥ 10 48% 15% 43% 3% 0.451
CLD ≥ 15 56% 8% 46% 1% 0.272
CLD ≥ 20 63% 5% 58% 1% 0.799
CLD ≥ 25 68% 4% 75% 1% 0.744