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Table 3 Validation and comparison to other methods in a gender benchmark dataset

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

C1 cannonical gene sets (MSigDB) GSOA GSEA GAGE GSAA
  Rank P FDR Rank P FDR Rank P FDR Rank P FDR
chrY 1 0.001 0.079 1 0.000 0.000 1 0.001 0.297 1 0.000 0.105
chrYq11 1 0.001 0.079 1 0.000 0.000 2 0.002 0.335 1 0.000 0.105
chrYp11 1 0.001 0.079 1 0.000 0.002 6 0.052 0.923 1 0.000 0.210
chrXq26 17 0.035 0.623 114 0.652 0.961 316 0.979 0.979 284 0.892 0.959
chrXp22 156 0.505 0.985 4 0.002 1.000 3 0.008 0.895 1 0.000 1
# of sig. gene sets 29 7 6 21
C2 cannonical gene sets (MsigDB)             
X-inactivation genes 17 0.031 0.770 1 0.000 0.000 2 0.008 0.914 1 0.000 0.135
Testis genes 71 0.127 0.885 1 0.000 0.067 3 0.008 0.914 1 0.000 0.890
GNF female genes 499 0.943 0.982 3 0.010 0.067 1 0.005 0.914 1 0.000 0.520
# of sig. gene sets 34 8 7 23
  1. We used the various methods to compare gene-expression levels between male and female cell lines