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

BMC Systems Biology

Table 7 Top 15 gene sets in 4th ranked superset in LUAD survival analysis

Gene Set Terms	P-value^a	gsScore	Weight^b
SWEET_LUNG_CANCER_KRAS_DN	0.7304	0.780	−0.185
ZHANG_BREAST_CANCER_PROGENITORS_UP	0.0248	0.256	0.096
ROZANOV_MMP14_TARGETS_UP	0.1038	0.161	0.103
MONNIER_POSTRADIATION_TUMOR_ESCAPE_DN	0.0058	0.157	−0.117
ACEVEDO_FGFR1_TARGETS_IN_PROSTATE_CANCER_MODEL_DN	0.0988	0.154	0.114
YOSHIMURA_MAPK8_TARGETS_DN	0.0195	0.150	−0.126
DELYS_THYROID_CANCER_DN	0.0065	0.125	−0.079
SWEET_LUNG_CANCER_KRAS_UP	0.2762	0.122	0.141
OSWALD_HEMATOPOIETIC_STEM_CELL_IN_COLLAGEN_GEL_DN	0.0132	0.101	0.120
GROSS_HYPOXIA_VIA_ELK3_UP	5.21 × 10⁻⁴	0.100	0.058
WATTEL_AUTONOMOUS_THYROID_ADENOMA_UP	0.1555	0.096	−0.089
VERHAAK_GLIOBLASTOMA_MESENCHYMAL	0.7314	0.095	0.113
PHONG_TNF_RESPONSE_NOT_VIA_P38	0.0972	0.093	−0.121
RUTELLA_RESPONSE_TO_HGF_UP	0.7217	0.091	−0.055
IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP	0.0249	0.090	0.088

^aThe P-value of gene set log-rank. ^bThe weight in the model corresponding to the connection of a gene set to the superset

ISSN: 1752-0509