Table 1 Approaches for lncRNA function prediction

Comparative genomics

The lncRNA transcripts that are conserved in both human and mouse, and located within or close to a coding gene in < 1 kb distance assumed to have close functional relationship with the neighboring gene. This method of predicting lncRNAs is may not be widely applied to genomic level due to the low conservation potential of lncRNAs.

[30]

Coexpression of lncRNA and coding genes

The lncRNAs and protein coding genes coexpressed in specific biological process regulation. The method is well practiced to predict and identify the enriched function of the lncRNAs at the genomic level.

[11]

Interaction with miRNAs and proteins

The lncRNAs may involve in regulatory network by coordinating with target sites of miRNA. Scientists developed different methods to determine the target sites of miRNA in lncRNAs such as miRcode interface helping the microRNA-lncRNA interaction study across the GENCODE annotated transcriptome, Validated RNA mediated interactions in genome-wide networks in determining the mediatory roles of lncRNA and its interaction and correlation in miRNA, mRNA and proteins which may help in predicting the lncRNA function. This approach is successful for those lncRNAs with known mechanism of interaction between miRNA and protein.

[31]