Measures of co-expression for improved function prediction of long non-coding RNAs

Almost 16,000 human long non-coding RNA (lncRNA) genes have been identified in the GENCODE project. However, the function of most of them remains to be discovered. The function of lncRNAs and other novel genes can be predicted by identifying significantly enriched annotation terms in already annotated genes that are co-expressed with the lncRNAs. However, such approaches are sensitive to the methods that are used to estimate the level of co-expression.

Researchers from the University of Zabol have tested and compared two well-known statistical metrics (Pearson and Spearman) and two geometrical metrics (Sobolev and Fisher) for identification of the co-expressed genes, using experimental expression data across 19 normal human tissues. They have also used a benchmarking approach based on semantic similarity to evaluate how well these methods are able to predict annotation terms, using a well-annotated set of protein-coding genes.

GO terms for a manually annotated set of 37 lncRNAs from FuncPred has been predicted using LNCRNA2GOA, FuncPred and LncRNA2Function, and the number of successful predictions has been counted

This work shows that geometrical metrics, in particular in combination with the statistical metrics, will predict annotation terms more efficiently than traditional approaches. Tests on selected lncRNAs confirm that it is possible to predict the function of these genes given a reliable set of expression data. The software used for this investigation is freely available.

Availability – A software implementation in R is available for download via GitHub, at LNCRNA2GOA [https://github.com/RezvanEhsani/LNCRNA2GOA]

Ehsani R, Drabløs F. (2019) Measures of co-expression for improved function prediction of long non-coding RNAs. BMC Bioinformatics 19(1):533. [article]

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