Table 5. Top 20 positive correlations identified by GSEA compared with PMT versus RST.
| Gene Set | Description |
|---|---|
| CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP | Genes upregulated in luminal-like breast cancer cell lines compared with the mesenchymal-like ones |
| COLDREN_GEFITINIB_RESISTANCE_DN | Genes downregulated in NSCLC cell lines resistant to gefitinib compared with the sensitive ones |
| CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_UP | Genes upregulated in basal-like breast cancer cell lines as compared with the mesenchymal-like ones |
| JAEGER_METASTASIS_DN | Genes downregulated in metastases from malignant melanoma compared with the primary tumors |
| LANDIS_ERBB2_BREAST_TUMORS_324_UP | The 324 genes identified by two analytical methods as changed in the mammary tumors induced by transgenic ERBB2 |
| MCBRYAN_PUBERTAL_BREAST_4_5WK_UP | Genes upregulated during pubertal mammary gland development between weeks 4 and 5 |
| LANDIS_BREAST_CANCER_PROGRESSION_UP | Genes upregulated in preneoplastic mammary tissue and whose expression is maintained in tumors |
| ONDER_CDH1_TARGETS_2_DN | Genes downregulated in HMLE cells (immortalized nontransformed mammary epithelium) after E-cadherin knockdown by RNAi |
| AIGNER_ZEB1_TARGETS | Genes upregulated in MDA-MB-231 cells (breast cancer) after knockdown of ZEB1 by RNAi |
| LIEN_BREAST_CARCINOMA_METAPLASTIC_VS_DUCTAL_DN | Genes downregulated between two breast carcinoma subtypes: metaplastic (MCB) and ductal (DCB) |
| MCBRYAN_PUBERTAL_BREAST_3_4WK_UP | Genes upregulated during pubertal mammary gland development between weeks 3 and 4 |
| REACTOME_TIGHT_JUNCTION_INTERACTIONS | Genes involved in tight junction interactions |
| SMID_BREAST_CANCER_ERBB2_UP | Genes upregulated in the ERBB2 subtype of breast cancer samples, characterized by higher expression of ERBB2 |
| WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_UP | Genes upregulated in mucinous ovarian carcinoma tumors of grades 1 and 2 compared with the normal surface epithelium tissue |
| SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_DN | Genes downregulated in IDC relative to DCIS (noninvasive) |
| SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN | Genes downregulated in nasopharyngeal carcinoma relative to the normal tissue |
| WAMUNYOKOLI_OVARIAN_CANCER_LMP_UP | Genes upregulated in mucinous ovarian carcinoma tumors of LMP compared with normal ovarian surface epithelium tissue |
| ROY_WOUND_BLOOD_VESSEL_DN | Genes downregulated in blood vessel cells from wound site |
| TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_LOBULAR_NORMAL_UP | Genes upregulated in lobular carcinoma versus normal lobular breast cells |
| KEGG_OXIDATIVE_PHOSPHORYLATION | Oxidative phosphorylation |
Abbreviations: DCIS, ductal carcinoma in situ; GSEA, gene signature enrichment analysis; IDC, invasive ductal carcinoma; LMP, low malignant potential; NSCLC; non-small-cell lung carcinoma; PMT, primary mammary tumor; RNAi, RNA interference; RST, recurrent spindle tumor.
False discovery rate (FDR) for all of the above sets was 0.000.