Inferring plant microRNA functional similarity using a weighted protein-protein interaction network.

Jun Meng,Dong Liu,Yushi Luan

doi:10.1186/s12859-015-0789-4

Jun Meng, Dong Liu + Show 1 more

Open Access

https://doi.org/10.1186/s12859-015-0789-4

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Abstract

BackgroundMiRNAs play a critical role in the response of plants to abiotic and biotic stress. However, the functions of most plant miRNAs remain unknown. Inferring these functions from miRNA functional similarity would thus be useful. This study proposes a new method, called PPImiRFS, for inferring miRNA functional similarity.ResultsThe functional similarity of miRNAs was inferred from the functional similarity of their target gene sets. A protein-protein interaction network with semantic similarity weights of edges generated using Gene Ontology terms was constructed to infer the functional similarity between two target genes that belong to two different miRNAs, and the score for functional similarity was calculated using the weighted shortest path for the two target genes through the whole network. The experimental results showed that the proposed method was more effective and reliable than previous methods (miRFunSim and GOSemSim) applied to Arabidopsis thaliana. Additionally, miRNAs responding to the same type of stress had higher functional similarity than miRNAs responding to different types of stress.ConclusionsFor the first time, a protein-protein interaction network with semantic similarity weights generated using Gene Ontology terms was employed to calculate the functional similarity of plant miRNAs. A novel method based on calculating the weighted shortest path between two target genes was introduced.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0789-4) contains supplementary material, which is available to authorized users.

Highlights

MiRNAs play a critical role in the response of plants to abiotic and biotic stress
This study proposes a novel computational method, called PPImiRFS, to obtain the functional similarity scores of miRNA pairs based on a protein-protein interaction network (PPIN) with semantic similarity weights generated using Gene Ontology (GO) terms and graph theoretic properties
To evaluate the reliability of the functional similarity scores computed by the PPImiRFS method, we divided all of the A. thaliana miRNAs into three classes: intrafamily, interfamily and randomly selected miRNA pairs

Summary

Introduction

The functions of most plant miRNAs remain unknown. Inferring these functions from miRNA functional similarity would be useful. This study proposes a new method, called PPImiRFS, for inferring miRNA functional similarity. MicroRNAs (miRNAs) are single-stranded noncoding RNAs and are typically ~22 nucleotides long. These molecules are involved in post-transcriptional regulation and trigger targeted degradation of messenger RNA or inhibit translation [1, 2]. The expression of miRNA genes is a multistep process. The miRNA gene is initially transcribed as a primary miRNA sequence (pri-miRNA) by RNA polymerase II. The pri-miRNA is processed into a hairpin sequence (precursor miRNA) by the endoribonuclease Dicer. The miRNA* strand is degraded, and the other miRNA strand, named the mature miRNA, is incorporated into the RNA-induced silencing complex (RISC) [3]

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