title: Inferring plant microRNA functional similarity using a weighted protein-protein interaction network.
abstract: MiRNAs 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.
  
  
  
  The 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.
  
  
  
  For 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.
authors.affiliation: School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning, China. mengjun@dlut.edu.cn.
authors.forename: Jun
authors.initials: J
authors.lastname: Meng
authors.affiliation: School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning, China. kobe_liudong@mail.dlut.edu.cn.
authors.forename: Dong
authors.initials: D
authors.lastname: Liu
authors.affiliation: School of Life Science and Biotechnology, Dalian University of Technology, Dalian, Liaoning, China. luanyush@dlut.edu.cn.
authors.forename: Yushi
authors.initials: Y
authors.lastname: Luan
mesh_terms: D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics*; D017343:Genes, Plant; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D060066:Protein Interaction Maps; D012372:ROC Curve; D012965:Sodium Chloride / Q000494:pharmacology; D012984:Software; D013312:Stress, Physiological / Q000187:drug effects / Q000235:genetics
chemical_list: D035683:MicroRNAs; D012965:Sodium Chloride