Table 1.

Overview of Categories and Corresponding Method/Tool for Acquiring lncRNA-lncRNA Association

Categories	Method/Tool	Data Types	Data Resources	References
Sequence similarity	EMBOSS Needle tool	lncRNA sequence	LncRNADisease, UCSC, LNCipedia	Needleman and Wunsch34
Functional similarity	LNCSIM	lncRNA-disease association, MeSH descriptors	LncRNADisease, Lnc2Cancer, MNDR, MeSH	Chen et al.35
Functional similarity	ILNCSIM	lncRNA-disease association, MeSH descriptors	MNDR, Lnc2Cancer, MeSH	Huang et al.36
Functional similarity	NA	lncRNA-gene association, protein-protein interaction	LncRNA2Target, StarBase, HPRD	Paik et al.37
Functional similarity	NA	lncRNA-miRNA association	StarBase	Zhao et al.40
Expression similarity	Spearman/Pearson correlation	lncRNA expression profiles	Array Express, UCSC Genome Bioinformatics	Chen and Yan41
Cosine similarity	cosine similarity	lncRNA-disease association	MNDR, Lnc2Cancer, LncRNADisease	Cheng et al.42

NA, not applicable.