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Table 2 Validation and comparison to other methods in a p53 benchmark microarray dataset

From: Inferring pathway dysregulation in cancers from multiple types of omic data

  GSOA GSEA GAGE GSAA
Canonical gene sets Rank P FDR Rank P FDR Rank P FDR Rank P FDR
P53 pathway 1 0.001 0.037 1 0.000 0.009 26 0.093 0.822 1 0.000 0.566
P53 signaling 15 0.002 0.058 21 0.028 0.614 30 0.109 0.822 29 0.048 0.695
P53 hypoxia pathway 1 0.001 0.037 1 0.000 0.009 27 0.103 0.822 5 0.002 0.713
P53 up 1 0.001 0.037 1 0.000 0.065 20 0.083 0.822 1 0.000 0.595
DNA damage signaling 1 0.001 0.037 80 0.223 1 5 0.043 0.822 40 0.061 0.693
Radiation sensitivity 1 0.001 0.037 6 0.002 0.088 18 0.077 0.822 11 0.014 0.621
Cell cycle regulator 1 0.001 0.037 116 0.330 1 4 0.042 0.822 20 0.030 0.571
Cell cycle pathway 1 0.001 0.037 237 0.729 0.949 17 0.075 0.822 55 0.104 0.593
Cell cycle 15 0.002 0.058 172 0.531 0.930 7 0.046 0.822 93 0.175 1
Cell cycle arrest 43 0.021 0.255 166 0.509 0.887 41 0.141 0.822 216 0.396 1
Ras pathway 39 0.016 0.209 7 0.002 0.284 64 0.186 0.822 312 0.565 1
MAPK cascade 50 0.040 0.418 16 0.021 0.494 57 0.177 0.822 107 0.204 1
# of sig. gene sets 62 32 10 39
  1. Each method identified pathways related to p53 signaling and cell-cycle regulation. The ranks for these pathways were generally lower for GSOA than for the competing methods