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Table 7 Statistical validation of the different gene prioritization strategies employed in this work (independently and in combination). Hypergeometric test, random bootstrap sampling experiment and enrichment features of the different gene prioritization strategies

From: Efficient and biologically relevant consensus strategy for Parkinson’s disease gene prioritization

  Hypergeometric Test Random Bootstrap Sampling (100 Generations) Enrichment
  n m p-value Mean Median Min. Max. Std. Dev. p-value (W) Fold-Enrichment TP Rate
Limma 134 10 0.0295 5.0410 5 0 17 2.1852 <0.0001 1.9837 0.0746
ML 168 11 0.0520 6.3211 6 0 22 2.4421 <0.0001 1.7402 0.0655
ML Limma 246 14 0.0805 9.2609 9 0 25 2.9426 <0.0001 1.5117 0.0569
PD_02 1437 73 0.0034 55.4259 55 25 87 6.6392 <0.0001 1.3171 0.0508
PD_07 494 26 0.0512 18.5957 18 2 41 4.1038 <0.0001 1.3982 0.0526
PD_02 PD_07 1931 99 0.0003 72.6709 73 37 112 7.3516 <0.0001 1.3623 0.0513
Concensus 50 7 0.0025 1.8817 2 0 10 1.3407 <0.0001 3.7200 0.1400
  1. n: number or genes in the prioritized PD module; m: number of known PD related genes in GAD found in the prioritized module; p-value: hypergeometric probability of finding by chance k or more known PD related genes in a set of n prioritized genes; Mean/Median/Min./Max./Std. Dev.: average/median/minimum/maximum/standard deviation of the number of known PD related genes in GAD included in randomly selected gene sets with the same number of genes as the corresponding set of prioritized genes; Fold-enrichment: fold difference between m and Mean (Fold-enrichment = m/Mean); TP Rate: ratio of known PD related genes in n (TP Rate = m/n)
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