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Table 2 Application of PAGE to different Affymetrix probe level analysis methods

From: PAGE: Parametric Analysis of Gene Set Enrichment

MAS5 MBEI RMA
Gene Set Z score p-value Gene Set Z score p-value Gene Set Z score p-value
Inflammatory Response Pathway 7.5051 <1.0E-12 Inflammatory Responses 7.5195 5.51E-14 Inflammatory Responses 7.3487 2.00E-13
Eicosanoid Synthesis 6.5925 <1.0E-12 Eicosanoid Synthesis 3.8957 9.79E-05 Eicosanoid Synthesis 4.1557 3.24E-05
Complement Activation Classical 3.0382 0.0024 Complement Activation 3.5487 0.0004 TGF-β Signaling Pathway 3.0438 0.0023
Nucleotide Metabolism 2.0536 0.0400 Nucleotide Metabolism 2.4207 0.0155 Complement Activation Classical 2.9402 0.0033
TGF-β Signaling Pathway 1.9758 0.0482 TGF-β Signaling Pathway 2.2379 0.0250 Nucleotide Metabolism 2.5867 0.0097
MAPK Cascade -2.2529 0.0243 Glutamate Metabolism -1.7249 0.0846 GPCRs Class A Rhodopsin-like -1.9907 0.0465
Translation Factors -2.3124 0.0208 MAPK Cascade -1.8685 0.0617 MAPK Cascade -2.1306 0.0331
Krebs-TCA Cycle -3.2551 0.0011 Proteasome Degradation -1.9605 0.0499 Krebs-TCA Cycle -2.6076 0.0091
Glycogen Metabolism -3.3488 0.0008 Krebs-TCA Cycle -2.1182 0.0342 Proteasome Degradation -2.7822 0.0054
Proteasome Degradation -3.7468 0.0002 Glycogen Metabolism -2.8330 0.0046 Glycogen Metabolism -2.9328 0.0034
Fatty Acid Degradation -3.8286 0.0001 Fatty Acid Degradation -2.8570 0.0043 Fatty Acid Degradation -3.4024 0.0007
Nuclear Receptors -4.2579 2.06E-05 Nuclear Receptors -3.4686 0.0005 Nuclear Receptors -4.1600 3.18E-05
Electron Transport Chain -6.3789 1.78E-10 Electron Transport Chain -4.2009 2.66E-05 Electron Transport Chain -5.1177 3.09E-07