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

BMC Systems Biology

Table 3 Top 15 gene sets in down-superset #1 in BRCA subtype analysis

Gene Set Terms	PScore ^a	gsScore	Weight^b
PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7	92.578	0.997	0.166
VANTVEER_BREAST_CANCER_ESR1_DN	80.186	0.811	−0.185
LEI_MYB_TARGETS	55.903	0.800	0.201
DOANE_BREAST_CANCER_ESR1_DN	87.537	0.644	−0.114
CUI_TCF21_TARGETS_2_UP	81.999	0.511	−0.103
ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN	46.415	0.340	0.127
DELACROIX_RARG_BOUND_MEF	55.442	0.336	0.141
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP	37.512	0.230	−0.074
FRASOR_RESPONSE_TO_ESTRADIOL_DN	77.02	0.218	0.108
HATADA_METHYLATED_IN_LUNG_CANCER_UP	76.111	0.215	0.066
SMID_BREAST_CANCER_LUMINAL_A_UP	51.385	0.211	0.077
FOSTER_KDM1A_TARGETS_UP	62.021	0.188	0.091
SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12	6.764	0.178	−0.096
SWEET_LUNG_CANCER_KRAS_UP	6.548	0.178	0.138
KOYAMA_SEMA3B_TARGETS_DN	24.534	0.176	0.094

^aThe PScore of gene set Mann Whitney U test
^bThe weight in the model corresponding to the connection of a gene set to the superset

ISSN: 1752-0509