Inferring plant microRNA functional similarity using a weighted protein-protein interaction network.
Inferring plant microRNA functional similarity using a weighted protein-protein interaction network.
复制标题
使用加权蛋白质-蛋白质相互作用网络推断植物 microRNA 功能相似性
DOI：
10.1186/s12859-015-0789-4
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发表时间：
2015-11-04
影响因子：
3
通讯作者：
Luan Y
中科院分区：
文献类型：
--
作者：
Meng J;Liu D;Luan Y
背景MiRNAs在植物对非生物胁迫和生物胁迫的响应中起着关键作用。然而，大多数植物miRNAs的功能仍然未知。因此，从miRNA功能相似性推断这些功能将是有用的。这项研究提出了一种新的方法，称为PPIMiRFS，用于推断miRNA的功能similarity.ResultsThe功能相似性的miRNA推断其靶基因集的功能相似性。构建蛋白质-蛋白质相互作用网络，利用Gene Ontology术语生成边的语义相似性权重，以推断属于两种不同miRNA的两个靶基因之间的功能相似性，并使用两个靶基因在整个网络中的加权最短路径计算功能相似性得分。实验结果表明，该方法比以往的方法（miRFunSim和GOSemSim）更有效、更可靠。此外，响应于相同类型的压力比响应于不同类型的stress.ConclusionsFor第一次，一个蛋白质-蛋白质相互作用网络的语义相似性权重使用基因本体论术语来计算植物miRNA的功能相似性的miRNA响应相同类型的压力有更高的功能相似性。提出了一种新的基于加权最短路径算法的两个目标基因之间的距离估计方法。
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 toArabidopsis 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.