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Table 2 Comparison between GAGE, PAGE and GSEA results from the two lung cancer datasets

From: GAGE: generally applicable gene set enrichment for pathway analysis

Gene Sets & Methods   Overlap Top 10 p-values Metastasis Tumor Sign. Sets
Experimental Sets GAGE 4 4.2E-35, 2.4E-13 3, 5 6, 7 242 (283), 120 (124)
  PAGE 4 1.0E-170, 2.0E-85 6, 4 8, 6 698 (757), 585 (655)
  GSEA 1 5.7E-3, 6.4E-3 1, 2 6, 4 3 (0), 4 (0)
Canonical Pathways GAGE 5 6.7E-6, 7.5E-4 10, 9 10, 9 20 (16), 10 (8)
  PAGE 4 4.2E-26, 3.7E-27 2, 3 4, 3 170 (202), 153 (186)
  GSEA 0 1.1E-2, 1.4E-2 1, 1 5, 5 2 (0), 4 (0)
  1. The top 10 most significantly enriched experimental sets and canonical pathways in poor clinical outcomes vs good outcomes were inferred by GAGE, PAGE, and GSEA from two published lung adenocarcinoma data sets used in the GSEA paper [3]. Data columns are overlap between top 10 gene sets for the two studies, top 10 p-values, number of top 10 gene sets related to metastasis (bt) and tumor (t and bt), and numbers of significant gene sets with p-value ≤ 0.001 (or FDR q-value ≤ 0. 01).