Table 6. Top 10 significant overlap gene set in MSigDB with top ranked 400 (approx) mRNA probes identified by alternative methods SAM, limma, and RF, as well as 374 mRNA probes identified by HO GSVD.
“BREAST_CANCER” was presented in bold to emphasize the overlap with breast cancer, whose counts are in parentheses at the right side of method names.
| SAM (1) | limma (0) | RF (0) | HO GSVD (5) | |
|---|---|---|---|---|
| 1 | BLALOCK_ALZHEIMERS_DISEASE_UP | PUJANA_BRCA1_PCC_NETWORK | DIAZ_CHRONIC_MEYLOGENOUS_LEUKEMIA_UP | SMID_BREAST_CANCER_LUMINAL_B_DN |
| 2 | SMID_BREAST_CANCER_NORMAL_LIKE_UP | BLALOCK_ALZHEIMERS_DISEASE_UP | BLALOCK_ALZHEIMERS_DISEASE_UP | SMID_BREAST_CANCER_BASAL_DN |
| 3 | SWEET_LUNG_CANCER_KRAS_DN | KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_UP | HAMAI_APOPTOSIS_VIA_TRAIL_UP | YOSHIMURA_MAPK8_TARGETS_UP |
| 4 | WEST_ADRENOCORTICAL_TUMOR_DN | RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP | PUJANA_BRCA1_PCC_NETWORK | SMID_BREAST_CANCER_RELAPSE_IN_BONE_DN |
| 5 | BOQUEST_STEM_CELL_CULTURED_VS_FRESH_UP | PUJANA_CHEK2_PCC_NETWORK | GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN | JAEGER_METASTASIS_DN |
| 6 | PUJANA_BRCA1_PCC_NETWORK | DIAZ_CHRONIC_MEYLOGENOUS_LEUKEMIA_UP | MILI_PSEUDOPODIA_HAPTOTAXIS_UP | GOZGIT_ESR1_TARGETS_DN |
| 7 | GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN | GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN | BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_UP | SMID_BREAST_CANCER_BASAL_UP |
| 8 | HAMAI_APOPTOSIS_VIA_TRAIL_UP | RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP | PUJANA_ATM_PCC_NETWORK | ONDER_CDH1_TARGETS_2_DN |
| 9 | BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_UP | FEVR_CTNNB_TARGETS_DN | PUJANA_CHEK2_PCC_NETWORK | SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_DN |
| 10 | PUJANA_CHEK2_PCC_NETWORK | CAIRO_HEPATOBLASTOMA_CLASSES_UP | BLALOCK_ALZHEIMERS_DISEASE_DN | FARMER_BREAST_CANCER_APOCRINE_VS_LUMINAL |