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

BMC Systems Biology

Table 6 Top 15 gene sets in the highest ranked superset in LUAD survival analysis

Gene Set Terms	P-value^a	gsScore	Weight^b
CUI_TCF21_TARGETS_2_UP	1.30 × 10^− 4	0.446	−0.211
RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN	2.02 × 10⁻⁴	0.254	−0.201
GROSS_HYPOXIA_VIA_ELK3_UP	5.21 × 10⁻⁴	0.245	0.115
KAAB_HEART_ATRIUM_VS_VENTRICLE_DN	5.10 × 10⁻⁴	0.194	0.145
MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN	0.0015	0.183	0.107
MITSIADES_RESPONSE_TO_APLIDIN_UP	0.2863	0.159	−0.171
KIM_WT1_TARGETS_DN	0.0064	0.146	0.081
ENK_UV_RESPONSE_EPIDERMIS_UP	1 × 10⁻⁵	0.143	0.077
SENESE_HDAC1_TARGETS_DN	0.8285	0.138	−0.162
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_UP	0.1411	0.129	−0.130
YANG_BCL3_TARGETS_UP	0.0299	0.126	0.163
GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN	0.9507	0.124	0.132
CONCANNON_APOPTOSIS_BY_EPOXOMICIN_DN	0.0264	0.112	0.147
SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP	0.0048	0.110	−0.051
RHEIN_ALL_GLUCOCORTICOID_THERAPY_DN	0.0154	0.107	0.051

^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