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Table 2 Results for of the pediatric AML analysis

From: Gene-set distance analysis (GSDA): a powerful tool for gene-set association analysis

Method Chloroma logWBC EFS
GSDA (t-test) 0.020 \(< 10^{-29}\) 0.060
GSDA (perm) 0.029 \(<10^{-6}\) 0.051
GSEA 0.030 0.008 0.572
GSA 0.512 0.688 0.114
SAFE 0.561 0.014 0.336
GT 0.014 \(< 10^{-5}\) 0.250
TOTS 0.960 \(< 0.001\) 0.217
POST 0.027 \(< 10^{-5}\) 0.130
PIANO (Wilcoxon)* 0.804 0.004 0.209
PIANO (Fisher)* 0.0004 \(< 10^{-37}\) 0.092
PIANO (Stouffer)* 0.004 \(< 10^{-27}\) 0.164
PIANO (Reporter)* 0.742 0.004 0.288
PIANO (Tail Strength)* 0.744 0.016 0.239
PIANO (Mean)* 0.836 0.030 0.217
PIANO (Median)* 0.834 0.001 0.316
PIANO (Sum)* 0.858 0.042 0.221
PIANO (MaxMean)* 0.116 0.011 1.000
PIANO (GSEA)* 0.039 0.028 1.000
PIANO (FGSEA)* 0.014 0.029 1.000
PIANO (PAGE)* 0.044 0.096 0.112
  1. The table shows the p values for each method for the association the expression of the KEGG AML pathway with clinical characteristics and survival in pediatric AML
  2. *PIANO was performed with only the gene-level statistics with signifMethod=’nullDist’ for Wilcoxon, Fisher, Stouffer, and Reporter methods and signifMethod = ‘geneSampling’ and 999 permutations for the other methods