Table 6. Top 20 negative correlations identified by GSEA compared with PMT versus RST.
| SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP | Genes upregulated in IDC relative to DCIS (noninvasive) |
| CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_DN | Genes downregulated in luminal-like breast cancer cell lines compared with the mesenchymal-like ones |
| REN_ALVEOLAR_RHABDOMYOSARCOMA_DN | Genes commonly downregulated in human ARMS and its mouse model overexpressing PAX3–FOXO1 fusion |
| LINDGREN_BLADDER_CANCER_CLUSTER_2B | Genes specifically upregulated in cluster IIb of UCC tumors |
| HOSHIDA_LIVER_CANCER_SUBCLASS_s1 | Genes from ‘subtype S1' signature of HCC: aberrant activation of the WNT signaling pathway |
| CLASPER_LYMPHATIC_VESSELS_DURING_METASTASIS_DN | Selected genes downregulated during invasion of lymphatic vessels during metastasis |
| POOLA_INVASIVE_BREAST_CANCER_UP | Genes upregulated in atypical ductal hyperplastic tissues from patients with (ADHC) breast cancer versus those without cancer (ADH) |
| ONDER_CDH1_TARGETS_2_UP | Genes upregulated in HMLE cells (immortalized nontransformed mammary epithelium) after E-cadherin (CDH1) knockdown by RNAi |
| RODWELL_AGING_KIDNEY_UP | Genes whose expression increases with age in normal kidney |
| REACTOME_CELL_CYCLE_MITOTIC | Genes involved in cell cycle, mitotic |
| CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_UP | Genes upregulated in transformed NIH3T3 cells (fibroblasts transformed by activated KRAS) versus normal cells |
| REACTOME_MITOTIC_M_M_G1_PHASES | Genes involved in mitotic M-M/G1 phases |
| NAKAYAMA_SOFT_TISSUE_TUMORS_PCA1_UP | Top 100 probe sets contributing to the positive side of the first principal component; predominantly associated with spindle cell and pleomorphic sarcoma samples |
| VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_UP | Upregulated genes distinguishing between two subtypes of gastric cancer: advanced (AGC) and early (EGC) |
| REACTOME_MITOTIC_PROMETAPHASE | Genes involved in mitotic prometaphase |
| MITSIADES_RESPONSE_TO_APLIDIN_DN | Genes downregulated in the MM1A cells (multiple myeloma) after treatment with aplidin, a marine-derived compound with potential anticancer properties |
| PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP | Upregulated genes in AILT compared with normal T lymphocytes |
| WALLACE_PROSTATE_CANCER_RACE_UP | Genes upregulated in prostate cancer samples from African-American patients compared with those from the European-American patients |
| REACTOME_G2_M_TRANSITION | Genes involved in G2/M transition |
| RAMALHO_STEMNESS_DN | Genes depleted in embryonic, neural and hematopoietic stem cells |
Abbreviations: ADH, atypical ductal hyperplasia; ADHC, atypical ductal hyperplastic cancer; AILT, angioimmunoblastic lymphoma; ARMS, alveolar rhabdomyosarcoma; DCIS, ductal carcinoma in situ; GSEA, gene signature enrichment analysis; HCC, hepatocellular carcinoma; IDC, invasive ductal carcinoma; PMT, primary mammary tumor; RNAi, RNA interference; RST, recurrent spindle tumor; UCC, urothelial cell carcinoma.
False discovery rate (FDR) for all of the above sets was 0.000.