Detecting composite functional module in miRNA regulation and mRNA interaction network

DOI10.3390/A10040136MaRDI QIDQ2633222zbMATH OpenOpenAlexFDO

Authors Yi Yang, Chu Pan

Publication date 8 May 2019

Published in Algorithms (Search for Journal in Brave)

Copyright license Creative Commons Attribution 4.0 International

Full work available at URL https://doi.org/10.3390/a10040136

zbMATH Keywords

composite miRNA functional modulemaximal bicliquesR-pairs

Mathematics Subject Classification ID

Applications of graph theory (05C90) Applications of statistics to biology and medical sciences; meta analysis (62P10) Graph theory (including graph drawing) in computer science (68R10) Biochemistry, molecular biology (92C40)

Review text

Summary: The detection of composite miRNA functional module (CMFM) is of tremendous significance and helps in understanding the organization, regulation and execution of cell processes in cancer, but how to identify functional CMFMs is still a computational challenge. In this paper we propose a novel module detection method called MBCFM (detecting Composite Function Modules based on Maximal Biclique enumeration), specifically designed to bicluster miRNAs and target messenger RNAs (mRNAs) on the basis of multiple biological interaction information and topical network features. In this method, we employ algorithm MICA to enumerate all maximal bicliques and further extract R-pairs from the miRNA-mRNA regulatory network. Compared with two existing methods, Mirsynergy and SNMNMF on ovarian cancer dataset, the proposed method of MBCFM is not only able to extract cohesiveness-preserved CMFMs but also has high efficiency in running time. More importantly, MBCFM can be applied to detect other cancer-associated miRNA functional modules.

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Cites work

• Consensus algorithms for the generation of all maximal bicliques
• scientific article; zbMATH DE number 845714 (Why is no real title available?)

Cited in

(4)

• Predicting miRNA-lncRNA interactions and recognizing their regulatory roles in stress response of plants
• Portrait of tissue-specific coexpression networks of noncoding RNAs (miRNA and lncRNA) and mRNAs in normal tissues
• Identifying microRNA and gene expression networks using graph communities
• MicroRNA Regulatory Network: Structure and Function

Describes a project that uses

Uses Software

• Mirsynergy
• GOstats

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