Table 5 Application of gene set analysis methods to leukemia data [22].
From: Microarray-based gene set analysis: a comparison of current methods
Top Pathways | NP | AP |
|---|---|---|
GSEA-Category | Â | Â |
   Glycolysis/Gluconeogenesis | <5e-05 | <5e-05 |
   Focal adhesion | <5e-05 | <5e-05 |
   Tight junction | <5e-05 | <5e-05 |
   Leukocyte transendothelial migration | <5e-05 | <5e-05 |
   Regulation of actin cytoskeleton | <5e-05 | <5e-05 |
   ...... | ... | ... |
GSEA-limma | Â | Â |
   Hematopoietic cell lineage | <5e-05 | 0.034 |
   B cell receptor signaling pathway | <5e-05 | 0.034 |
   Glutathione metabolism | 0.017 | 1 |
   Glycolysis/Gluconeogenesis | 0.025 | 1 |
   Natural killer cell mediated cytotoxicity | 0.028 | 1 |
   ...... | ... | ... |
SAFE | Â | Â |
   Natural killer cell mediated cytotoxicity | 0.0052 | 1 |
   Glycolysis/Gluconeogenesis | 0.00835 | 1 |
   Galactose metabolism | 0.0128 | 1 |
   Pyrimidine metabolism | 0.0333 | 1 |
   Cell cycle | 0.0353 | 1 |
   ...... | ... | ... |
GlobalTest | Â | Â |
   Toll-like receptor signaling pathway | <5e-05 | <5e-05 |
   Jak-STAT signaling pathway | <5e-05 | <5e-05 |
   Focal adhesion | <5e-05 | <5e-05 |
   Tight junction | <5e-05 | <5e-05 |
   Leukocyte transendothelial migration | <5e-05 | <5e-05 |
   ...... | ... | ... |
PCOT2 | Â | Â |
   Jak-STAT signaling pathway | <5e-05 | 0.001 |
   Glycolysis Gluconeogenesis | <5e-05 | 0.001 |
   Focal adhesion | <5e-05 | 0.001 |
   Tight junction | <5e-05 | 0.001 |
   Hematopoietic cell lineage | <5e-05 | 0.001 |
   ...... | ... | ... |
sigPathway | Â | Â |
   Arachidonic acid metabolism | <5e-05 | 0.001 |
   Metabolism of xenobiotics by cytochrome P450 | <5e-05 | 0.004 |
   Glutathione metabolism | <5e-05 | 0.009 |
   Cell cycle | 0.0001 | 0.016 |
   Starch and sucrose metabolism | 0.0002 | 0.023 |
   ...... | ... | ... |