Skip to main content

Table 4 Significant gene sets of overlap between MSigDB and Selected Genes

From: ClearF: a supervised feature scoring method to find biomarkers using class-wise embedding and reconstruction

Gene Set Name (# Genes) Description # Genes in
Overlap
p-value FDR
q-value
SMID_BREAST_CANCER_BASAL_UP (648) Genes up-regulated in basal subtype of breast cancer samples. 13 7.43 e-17 7.85 e-13
NIKOLSKY_BREAST_CANCER_17Q11_Q21_AMPLIPLICON (133) Genes within amplicon 17q11-q21 identified in a copy number alterations study of 191 breast tumor samples. 9 1.47 e-16 7.85 e-13
FARMER_BREAST_CANCER_CLUSTER_8 (7) Cluster 8: selected ERBB2 (GeneID = 2064) amplicon genes clustered together across breast cancer samples. 5 1.75 e-15 6.23 e-12
VANTVEER_BREAST_CANCER_ESR1_DN (240) Down-regulated genes from the optimal set of 550 markers discriminating breast cancer samples by ESR1 (GeneID = 2099) expression: ER(+) vs ER(−) tumors. 9 3.23 e-14 8.16 e-11
SMID_BREAST_CANCER_LUMINAL_B_DN (564) Genes down-regulated in the luminal B subtype of breast cancer. 11 3.82 e-14 8.16 e-11
SMID_BREAST_CANCER_ERBB2_UP (147) Genes up-regulated in the erbb2 subype of breast cancer samples, characterized by higher expression of ERBB2 (GeneID = 2064). 7 5.68 e-12 1.01 e-8
FARMER_BREAST_CANCER_BASAL_VS_LULMINAL (330) Genes which best discriminated between two groups of breast cancer according to the status of ESR1 and AR (GeneID = 2099;367): basal (ESR1- AR-) and luminal (ESR1+ AR+). 8 3.31 e-11 5.05 e-8
SMID_BREAST_CANCER_RELAPSE_IN_BONE_DN (315) Genes down-regulated in bone relapse of breast cancer. 7 1.18 e-9 1.58 e-6
DOANE_BREAST_CANCER_ESR1_DN (48) Genes down-regulated in breast cancer samples positive for ESR1 (GeneID = 2099) compared to the ESR1 negative tumors. 4 2.81 e-8 3.34 e-5
FONTAINE_PAPILLARY_THYROID_CARCINOMA_UA_UP (66) Genes up-regulated in papillary thyroid carcinoma (PTC) compared to other thyroid tumors. 4 1.03 e-7 1.1 e-4