Table 2.

The computational methods included in this study

Abbreviation	# RNA	Cohort	Applicable data	Purpose	References
CC	–	BC	Multi-omics	Subtyping	[6]
CNMF	–	BC	Multi-omics	Subtyping	[7]
iCluster	–	BC	Multi-omics	Subtyping	[8]
IntClust	—	BC	mRNAs	${\text{Subtyping}}^1$	[9]
SNF	–	BC	Multi-omics	Subtyping	[10]
SNF-CC	–	BC	Multi-omics	subtyping	[25]
WSNF	–	BC	mRNAs, miRNAs	Subtyping	[11]
CIMLR	–	BC	Multi-omics	Subtyping	[12]
PINS	–	BC	Multi-omics	Subtyping	[13]
NEMO	–	BC	Multi-omics	Subtyping	[14]
intNMF	–	BC	Multi-omics	Subtyping	[67]
PAM50	50	BC	mRNAs	${\text{Subtyping}}^1$	[15]
rorS	50	BC	mRNAs	Prognosis	[15]
GENE70	70	ER+	mRNAs	Prognosis	[16]
OncotypeDX	21	ER+	mRNAs	Prognosis	[17]
GGI	97	ER+	mRNAs	Prognosis	[18]
Tamr13	181	ER+	mRNAs	Prognosis	[19]
AURKA	1	BC	mRNA	Prognosis	[20]
ESR1	1	BC	mRNA	Prognosis	[20]
ERBB2	1	BC	mRNA	Prognosis	[20]
GENIUS	314	BC	mRNAs	Prognosis	[21]
PIK3CAGS	278	ER+	mRNAs	Prognosis	[22]
EndoPredict	11	ER+	mRNAs	Prognosis	[23]
Ensemble	238	BC	mRNAs	Prognosis	Additional file 1
miR-21	1	BC	miRNA	Prognosis	[69–71]
miR-155	1	BC	miRNA	Prognosis	[72]
miR-210	1	BC	miRNA	Prognosis	[73, 74]
RNAmodel	37	BC	mRNAs, miRNAs	Prognosis	[38]
miRNA10	10	BC	miRNAs	Prognosis	[43]
HOTAIR	1	BC	lncRNA	Prognosis	[75]
MALAT1	1	BC	lncRNA	Prognosis	[76]
DSCAM-AS1	1	BC	lncRNA	Prognosis	[77]
lncRNA12	12	BC	lncRNAs	Prognosis	[39]
LncRNA6	6	ER+	lncRNAs	Prognosis	[40]
LncRNA5	5	BC	lncRNAs	Prognosis	[41]

Abbreviations for prognostic methods are defined in Additional file 1. # RNA, number of RNA signatures used in methods; ${}^1$, the method maps breast cancer patients to predefined subtypes; mRNA, messenger RNA; miRNA, microRNA; lncRNA, long non-coding RNA; BC, breast cancer; ER+, estrogen receptor-positive breast cancer