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Table 3 GAGE applied to the BMP6-MSC dataset of small sample size

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

Experimental Sets t-statistic p-value q-value P.exp1 P.exp2
Ifna_Hcmv_6hrs_Up -3.80 2.9E-07 2.9E-04 3.7E-04 1.6E-04
Der_Ifnb_Up -3.47 1.6E-06 8.1E-04 3.3E-03 1.1E-04
Baf57_Bt549_Dn -3.09 1.4E-05 0.005 7.2E-03 5.2E-04
Ifn_Beta_Up -2.92 5.4E-05 0.012 1.2E-02 1.3E-03
Sana_Ifng_Endothelial_Up -2.88 6.6E-05 0.014 1.2E-02 1.7E-03
Ifn_Any_Up -2.76 1.1E-04 0.019 2.4E-02 1.4E-03
Dac_Bladder_Up -2.65 2.8E-04 0.036 2.4E-03 4.0E-02
Grandvaux_Ifn_Not_Irf3_Up -2.76 2.8E-04 0.037 3.8E-02 2.6E-03
Ifna_Uv-Cmv_Common_Hc -2.55 5.1E-04 0.056 1.6E-02 1.1E-02
Bennett_Sle_Up -2.48 7.3E-04 0.071 1.4E-02 2.0E-02
Canonical Pathways t-statistic p-value q-value P.exp1 P.exp2
Tgf_Beta_Signaling_Pathway 3.15 2.2E-05 0.009 1.2E-03 1.3E-03
Wnt_Signaling 2.47 5.9E-04 0.099 3.2E-03 1.7E-02
Alkpathway 2.46 8.8E-04 0.11 9.8E-03 8.7E-03
Proliferation_Genes 2.27 1.3E-03 0.13 6.8E-03 1.9E-02
Cell_Proliferation 2.24 1.5E-03 0.15 2.1E-02 7.5E-03
Hematopoesis_Related_Trans 2.05 3.9E-03 0.31 1.8E-02 2.5E-02
Erythpathway 1.98 7.5E-03 0.46 2.7E-02 3.5E-02
Smooth_Muscle_Contraction 1.79 1.0E-02 0.54 2.7E-02 5.2E-02
Apoptosis 1.73 1.3E-02 0.60 7.1E-02 2.5E-02
Breast_Cancer_Estrogen_Signaling 1.61 2.0E-02 0.69 8.1E-02 3.6E-02
  1. Top 10 most significantly differentially expressed experimental sets and canonical pathways were inferred by GAGE from human MSCs following an 8 hour BMP6 treatment. Two replicate experiments were done, each with BMP6 treated sample and control. Therefore GAGE was applied to each experiment and derived corresponding p-values (P.exp1–2). Gene sets were ranked based on global p-values from both experiments. FDR q-values were estimated to correct the global p-values for the multiple testing issue.