Mining plant endogenous target mimics from miRNA-lncRNA interactions based on dual-path parallel ensemble pruning method

This study proposes a novel ensemble pruning protocol for predicting plant miRNA-lncRNA interactions at first. It adaptively prunes the base models based on dual-path parallel ensemble method to meet the challenge of cross-species prediction. Then potential eTMs are mined from predicted results. The expression levels of RNAs are identified through biological experiment to construct the lncRNA-miRNA-mRNA regulatory network, and the functions of potential eTMs are inferred through enrichment analysis. Experiment results show that the proposed protocol outperforms existing methods and state-of-the-art predictors on various plant species. A total of 17 potential eTMs are verified by biological experiment to involve in 22 regulations, and 14 potential eTMs are inferred by Gene Ontology enrichment analysis to involve in 63 functions, which is significant for further research.PMID:34662389 | DOI:10.1093/bib/bbab440

Source: Briefings in Bioinformatics - October 18, 2021 Category: Bioinformatics Authors: Qiang Kang Jun Meng Chenglin Su Yushi Luan Source Type: research