Table 2. Overlap between mRNAs identified (S1 Table) and MSigDB.
Top 10 ranked gene sets are presented. Upper rows: type I, lower rows: type II tensors are considered in each gene set name, respectively. The word “BREAST_CANCER/_DUCTAL_CARCINOMA” was presented in bold face in order to emphasize the overlap with breast cancer related gene sets. K: The number of genes in each gene set, k: The number of genes overlapped.
| Gene Set Name | (K) | Description | (k) | k/K | p-value | FDR q-value |
|---|---|---|---|---|---|---|
| SMID_BREAST_CANCER_LUMINAL_B_DN | 564 | Genes down-regulated in the luminal B subtype of breast cancer. | 100 | 0.1773 | 4.00E-105 | 1.36E-101 |
| 88 | 0.1560 | 2.34E-090 | 7.94E-087 | |||
| SMID_BREAST_CANCER_BASAL_DN | 701 | Genes down-regulated in basal subtype of breast cancer samples. | 91 | 0.1298 | 2.06E-082 | 3.50E-079 |
| 86 | 0.1227 | 6.42E-079 | 1.09E-075 | |||
| DOANE_BREAST_CANCER_ESR1_UP | 112 | Genes up-regulated in breast cancer samples positive for ESR1 compared to the ESR1 negative tumors. | 44 | 0.3929 | 5.78E-063 | 6.56E-060 |
| 38 | 0.3393 | 6.29E-053 | 4.28E-050 | |||
| SMID_BREAST_CANCER_RELAPSE_IN_BONE_DN | 315 | Genes down-regulated in bone relapse of breast cancer. | — | — | — | — |
| 51 | 0.1619 | 1.17E-052 | 6.63E-050 | |||
| JAEGER_METASTASIS_DN | 258 | Genes down-regulated in metastases from malignant tumors. melanoma compared to the primar | — | — | — | — |
| 43 | 0.1667 | 5.25E-045 | 2.55E-042 | |||
| WALLACE_PROSTATE_CANCER_RACE_UP | 299 | Genes up-regulated in prostate cancer samples from African-American patients compared to those from the European-American patients. | 55 | 0.1839 | 5.86E-058 | 4.98E-055 |
| — | — | — | — | |||
| SMID_BREAST_CANCER_NORMAL_LIKE_UP | 476 | Genes up-regulated in the normal-like subtype of breast cancer. | 61 | 0.1282 | 2.40E-054 | 1.63E-051 |
| — | — | — | — | |||
| 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: basal (ESR1- AR-) and luminal (ESR1+ AR+). | 54 | 0.1636 | 5.31E-054 | 3.01E-051 |
| 54 | 0.1636 | 5.03E-056 | 4.27E-053 | |||
| POOLA_INVASIVE_BREAST_CANCER_UP | 288 | Genes up-regulated in atypical ductal hyperplastic tissues from patients with (ADHC) breast cancer vs those without the cancer (ADH). | 51 | 0.1771 | 7.55E-053 | 3.67E-050 |
| — | — | — | — | |||
| MCLACHLAN_DENTAL_CARIES_UP | 254 | Genes up-regulated in pulpal tissue extracted from carious teeth. | 47 | 0.1850 | 1.12E-049 | 4.77E-047 |
| — | — | — | — | |||
| SMID_BREAST_CANCER_BASAL_UP | 648 | Genes up-regulated in basal subtype of breast cancer samples. | 63 | 0.0972 | 1.38E-048 | 5.23E-046 |
| 78 | 0.1204 | 1.18E-070 | 1.34E-067 | |||
| SMID_BREAST_CANCER_LUMINAL_B_UP | 172 | Genes up-regulated in the luminal B subtype of breast cancer. | 38 | 0.2209 | 1.95E-043 | 6.63E-041 |
| 37 | 0.2151 | 3.29E-043 | 1.40E-040 | |||
| DELYS_THYROID_UP_CANCER | 443 | Genes up-regulated in papillary thyroid carcinoma (PTC) compared to normal tissue. | — | — | — | — |
| 48 | 0.1084 | 5.47E-041 | 2.07E-038 | |||
| TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_DUCTAL_NORMAL_DN | 198 | Genes down-regulated in ductal carcinoma vs normal ductal breast cells. | — | — | — | — |
| 36 | 0.1818 | 3.16E-039 | 1.08E-036 |