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Table 8 The statistical information of GSAE outputs between the training and test TCGA data sets of four cancer types

From: GSAE: an autoencoder with embedded gene-set nodes for genomics functional characterization

    Two proportion z-test
TCGA
data set
Superset
Jaccard Indexa
Gene set
Jaccard Indexb
Superset
Proportionc
Gene set
Proportiond
P-valuee
BRCA 0.344 0.124 11 / 24 31 / 197 0.0002
LUAD 0.182 0.113 6 / 12 32 / 145 0.0150
SKCM 0.179 0.069 5 / 19 17 / 139 0.0485
LGG 0.483 0.475 29 / 45 299 / 481 0.3821
  1. Supersets/gene sets with log-rank P-value < 0.05 were selected as prognostic significant sets. aJaccard index of significant supersets between training and test data. bJaccard index of significant gene sets between training and test data. cSuperset proportion: (# of overlapped significant supersets between training and test data) over (# of significant supersets in training data). dGene set proportion: (# of overlapped significant gene sets between training and test data) over (# of significant gene sets in training data). eThe P-value of z-test comparing superset and gene set proportions