title: Mirin: identifying microRNA regulatory modules in protein-protein interaction networks.
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.
  
  
  METHODS
  Mirin is freely available at http://mirin.ym.edu.tw/.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: 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.
authors.forename: Ken-Chi
authors.initials: KC
authors.lastname: Yang
authors.affiliation: 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.
authors.forename: Chia-Lang
authors.initials: CL
authors.lastname: Hsu
authors.affiliation: 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.
authors.forename: Chen-Ching
authors.initials: CC
authors.lastname: Lin
authors.affiliation: 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.
authors.forename: Hsueh-Fen
authors.initials: HF
authors.lastname: Juan
authors.affiliation: 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.
authors.forename: Hsuan-Cheng
authors.initials: HC
authors.lastname: Huang
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics / Q000378:metabolism; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006801:Humans; D035683:MicroRNAs / Q000378:metabolism*; D025941:Protein Interaction Mapping; D012333:RNA, Messenger / Q000378:metabolism; D012984:Software
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger