Open AccessConstruction and investigation of breast‐cancer‐specific ceRNA network based on the mRNA and miRNA expression data
Author(s) -
Zhou Xionghui,
Liu Juan,
Wang Wei
Publication year - 2014
Publication title -
iet systems biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.367
H-Index - 50
eISSN - 1751-8857
pISSN - 1751-8849
DOI - 10.1049/iet-syb.2013.0025
Subject(s) - microrna , breast cancer , competing endogenous rna , computational biology , messenger rna , biology , gene expression , cancer , bioinformatics , gene , genetics , rna , long non coding rna
It has been proved and widely acknowledged that messenger RNAs can talk to each other by competing for a limited pool of miRNAs. The competing endogenous RNAs are called as ceRNAs. Although some researchers have recently used ceRNAs to do biological function annotations, few of them have investigated the ceRNA network on specific disease systematically. In this work, using both miRNA expression data and mRNA expression data of breast cancer patient as well as the miRNA target relations, the authors proposed a computational method to construct a breast‐cancer‐specific ceRNA network by checking whether the shared miRNA sponges between the gene pairs are significant. The ceRNA network is shown to be scale‐free, thus the topological characters such as hub nodes and communities may provide important clues for the biological mechanism. Through investigation on the communities (the dense clusters) in the network, it was found that they are related to cancer hallmarks. In addition, through function annotation of the hub genes in the network, it was found that they are related to breast cancer. Moreover, classifiers based on the discriminative hubs can significantly distinguish breast cancer patients’ risks of distant metastasis in all the three independent data sets.