RNAenrich: a web server for non-coding RNA enrichment

Abstract

Abstract Motivation With the rapid advances of RNA sequencing and microarray technologies in non-coding RNA (ncRNA) research, functional tools that perform enrichment analysis for ncRNAs are needed. On the one hand, because of the rapidly growing interest in circRNAs, snoRNAs, and piRNAs, it is essential to develop tools for enrichment analysis for these newly emerged ncRNAs. On the other hand, due to the key role of ncRNAs’ interacting target in the determination of their function, the interactions between ncRNA and its corresponding target should be fully considered in functional enrichment. Based on the ncRNA–mRNA/protein-function strategy, some tools have been developed to functionally analyze a single type of ncRNA (the majority focuses on miRNA); in addition, some tools adopt predicted target data and lead to only low-confidence results. Results Herein, an online tool named RNAenrich was developed to enable the comprehensive and accurate enrichment analysis of ncRNAs. It is unique in (i) realizing the enrichment analysis for various RNA types in humans and mice, such as miRNA, lncRNA, circRNA, snoRNA, piRNA, and mRNA; (ii) extending the analysis by introducing millions of experimentally validated data of RNA–target interactions as a built-in database; and (iii) providing a comprehensive interacting network among various ncRNAs and targets to facilitate the mechanistic study of ncRNA function. Importantly, RNAenrich led to a more comprehensive and accurate enrichment analysis in a COVID-19-related miRNA case, which was largely attributed to its coverage of comprehensive ncRNA–target interactions. Availability and implementation RNAenrich is now freely accessible at https://idrblab.org/rnaenr/.