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Current Bioinformatics

Author(s): Lei Tian and Shu-Lin Wang*

DOI: 10.2174/1574893615999200711171530

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Exploring miRNA Sponge Networks of Breast Cancer by Combining miRNA-disease-lncRNA and miRNA-target Networks

Page: [385 - 394] Pages: 10

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Abstract

Background: Recently, ample researches show that microRNAs (miRNAs) not only interact with coding genes but interact with a pool of different RNAs. Those RNAs are called miRNA sponges, including long non-coding RNAs (lncRNAs), circular RNA, pseudogenes and various messenger RNAs. Understanding regulatory networks of miRNA sponges can better help researchers to study the mechanisms of breast cancers.

Objective: We develop a new method to explore miRNA sponge networks of breast cancer by combining miRNA-disease-lncRNA and miRNA-target networks (MSNMDL).

Methods: Firstly, MSNMDL infers miRNA-lncRNA functional similarity networks from miRNAdisease- lncRNA networks. Secondly, MSNMDL forms lncRNA-target networks by using lncRNA to replace the role of matched miRNA in miRNA-target networks according to the lncRNA-miRNA pair of miRNA-lncRNA functional similarity networks. And MSNMDL only retains the genes of breast cancer in lncRNA-target networks to construct candidate miRNA sponge networks. Thirdly, MSNMDL merges these candidate miRNA sponge networks with other miRNA sponge interactions and then selects top-hub lncRNA and its interactions to construct miRNA sponge networks.

Result: MSNMDL is superior to other methods in terms of biological significance and its identified modules might act as module signatures for prognostication of breast cancer.

Conclusion: MiRNA sponge networks identified by MSNMDL are biologically significant and are closely associated with breast cancer, which makes MSNMDL a promising way for researchers to study the pathogenesis of breast cancer.

Keywords: miRNA sponge networks, miRNA sponge modules, breast cancer, biological enrichment, clustering algorithm, prognostication.

Graphical Abstract

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