Mirin: identifying microRNA regulatory modules in protein-protein interaction networks

Ken-Chi Yang; Chia-Lang Hsu; Chen-Ching Lin; Hsueh-Fen Juan; Hsuan-Cheng Huang

doi:10.1093/bioinformatics/btu306

Mirin: identifying microRNA regulatory modules in protein-protein interaction networks

Bioinformatics. 2014 Sep 1;30(17):2527-8. doi: 10.1093/bioinformatics/btu306. Epub 2014 May 2.

Authors

Ken-Chi Yang¹, Chia-Lang Hsu¹, Chen-Ching Lin², Hsueh-Fen Juan³, Hsuan-Cheng Huang¹

Affiliations

¹ Institute of Biomedical Informatics, Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei 112, Department of Life Science, Graduate Institute of Biomedical Electronics and Bioinformatics and Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 106, Taiwan.
² Institute of Biomedical Informatics, Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei 112, Department of Life Science, Graduate Institute of Biomedical Electronics and Bioinformatics and Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 106, Taiwan Institute of Biomedical Informatics, Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei 112, Department of Life Science, Graduate Institute of Biomedical Electronics and Bioinformatics and Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 106, Taiwan.
³ Institute of Biomedical Informatics, Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei 112, Department of Life Science, Graduate Institute of Biomedical Electronics and Bioinformatics and Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 106, Taiwan Institute of Biomedical Informatics, Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei 112, Department of Life Science, Graduate Institute of Biomedical Electronics and Bioinformatics and Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 106, Taiwan Institute of Biomedical Informatics, Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei 112, Department of Life Science, Graduate Institute of Biomedical Electronics and Bioinformatics and Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 106, Taiwan.

PMID: 24794934
DOI: 10.1093/bioinformatics/btu306

Abstract

Exploring microRNA (miRNA) regulations and protein-protein interactions could reveal the molecular mechanisms responsible for complex biological processes. Mirin is a web-based application suitable for identifying functional modules from protein-protein interaction networks regulated by aberrant miRNAs under user-defined biological conditions such as cancers. The analysis involves combining miRNA regulations, protein-protein interactions between target genes, as well as mRNA and miRNA expression profiles provided by users. Mirin has successfully uncovered oncomirs and their regulatory networks in various cancers, such as gastric and breast cancer.

Availability and implementation: Mirin is freely available at http://mirin.ym.edu.tw/.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Breast Neoplasms / genetics
Breast Neoplasms / metabolism
Female
Gene Expression Regulation, Neoplastic*
Gene Regulatory Networks
Humans
MicroRNAs / metabolism*
Protein Interaction Mapping*
RNA, Messenger / metabolism
Software*

Substances

MicroRNAs
RNA, Messenger