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