Robust assignment of cancer subtypes from expression data using a uni-variate gene expression average as classifier

Table 1 Balanced accuracies of prediction obtained in various phenotypes using the metagene classifier (ROC) and linear SVM (SVM).

Phenotype/ Method	Training¹	Validation	Validation	Training	Validation	Validation	Training	Validation	Validation	Mean
ER ² (BC)	vandeVijver	WangY	Sotiriou	WangY	vandeVijver	Sotiriou	Sotiriou	vandeVijver	WangY
ROC	0.95	0.89	0.74	0.89	0.94	0.77	0.77	0.90	0.88	0.85
SVM	0.94	0.82	0.71	0.82	0.95	0.73	0.69	0.95	0.82	0.83
Grade ³ (BC)	vandeVijver	Sotiriou		Sotiriou	vandeVijver
ROC	0.79	0.85		0.84	0.82					0.84
SVM	0.72	0.78		0.84	0.78					0.78
Size ⁴ (BC)	vandeVijver	Sotiriou		Sotiriou	vandeVijver
ROC	0.63	0.65		0.70	0.60					0.63
SVM	0.57	0.51		0.61	0.48					0.49
MYCN ⁵ (NB)	WangQ	JanoueixL	Attiyeh	JanoueixL	WangQ	Attiyeh	Attiyeh	WangQ	JanoueixL
ROC	0.94	0.91	0.82	0.87	0.89	0.79	0.81	0.95	0.89	0.88
SVM	0.98	0.83	0.75	0.88	0.97	0.67	0.85	0.98	0.87	0.84
Stage ⁶ (NB)	WangQ	JanoueixL	Attiyeh	JanoueixL	WangQ	Attiyeh	Attiyeh	WangQ	JanoueixL
ROC	0.74	0.58	0.82	0.66	0.65	0.70	0.69	0.62	0.48	0.64
SVM	0.79	0.58	0.74	0.61	0.73	0.61	0.60	0.72	0.54	0.65
AD/SQ ⁷ (LC)	Angulo	Takeuchi		Takeuchi	Angulo
ROC	0.93	0.96		0.95	0.96					0.96
SVM	0.89	0.91		0.93	0.84					0.88
Grade ⁸ (LC)	Angulo	Takeuchi		Takeuchi	Angulo
ROC	0.67	0.69		0.69	0.68					0.68
SVM	0.63	0.64		0.63	0.59					0.61

¹ Accuracies given in italics indicates accuracies obtained in the training set using LOOCV
² ER+ vs. ER-
³ grade 1 vs. grade 3
⁴ tumors < = 2 cm vs. tumors > 2 cm
⁵ MYCN amplification positive vs. MYCN amplification negative
⁶ stage 1 and 2 vs. stage 3 and 4
⁷ adenocarcinoma vs. squamous cell carcinoma
⁸ grade 1 vs. grade 2 and 3
Abbreviations; BC = Breast Cancer, NB = Neuroblastoma, LC = Lung Cancer

ISSN: 1471-2407