title: Identifying cancer-related microRNAs based on gene expression data.
abstract: BACKGROUND
  MicroRNAs (miRNAs) are short non-coding RNAs that play important roles in post-transcriptional regulations as well as other important biological processes. Recently, accumulating evidences indicate that miRNAs are extensively involved in cancer. However, it is a big challenge to identify which miRNAs are related to which cancer considering the complex processes involved in tumors, where one miRNA may target hundreds or even thousands of genes and one gene may regulate multiple miRNAs. Despite integrative analysis of matched gene and miRNA expression data can help identify cancer-associated miRNAs, such kind of data is not commonly available. On the other hand, there are huge amount of gene expression data that are publicly accessible. It will significantly improve the efficiency of characterizing miRNA's function in cancer if we can identify cancer miRNAs directly from gene expression data.
  
  
  RESULTS
  We present a novel computational framework to identify the cancer-related miRNAs based solely on gene expression profiles without requiring either miRNA expression data or the matched gene and miRNA expression data. The results on multiple cancer datasets show that our proposed method can effectively identify cancer-related miRNAs with higher precision compared with other popular approaches. Furthermore, some of our novel predictions are validated by both differentially expressed miRNAs and evidences from literature, implying the predictive power of our proposed method. In addition, we construct a cancer-miRNA-pathway network, which can help explain how miRNAs are involved in cancer.
  
  
  METHODS
  The R code and data files for the proposed method are available at http://comp-sysbio.org/miR_Path/
  
  
  BACKGROUND
  liukeq@gmail.com
  
  
  BACKGROUND
  supplementary data are available at Bioinformatics online.
authors.affiliation: School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, LERIA, University of Angers, 49045 Angers Cedex 01, France, Department of Mathematics, Shanghai University, Shanghai 200444, China and Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Xing-Ming
authors.initials: XM
authors.lastname: Zhao
authors.affiliation: School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, LERIA, University of Angers, 49045 Angers Cedex 01, France, Department of Mathematics, Shanghai University, Shanghai 200444, China and Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, LERIA, University of Angers, 49045 Angers Cedex 01, France, Department of Mathematics, Shanghai University, Shanghai 200444, China and Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Ke-Qin
authors.initials: KQ
authors.lastname: Liu
authors.affiliation: School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, LERIA, University of Angers, 49045 Angers Cedex 01, France, Department of Mathematics, Shanghai University, Shanghai 200444, China and Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Guanghui
authors.initials: G
authors.lastname: Zhu
authors.affiliation: School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, LERIA, University of Angers, 49045 Angers Cedex 01, France, Department of Mathematics, Shanghai University, Shanghai 200444, China and Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Feng
authors.initials: F
authors.lastname: He
authors.affiliation: School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, LERIA, University of Angers, 49045 Angers Cedex 01, France, Department of Mathematics, Shanghai University, Shanghai 200444, China and Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Béatrice
authors.initials: B
authors.lastname: Duval
authors.affiliation: School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, LERIA, University of Angers, 49045 Angers Cedex 01, France, Department of Mathematics, Shanghai University, Shanghai 200444, China and Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Richer
authors.affiliation: School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, LERIA, University of Angers, 49045 Angers Cedex 01, France, Department of Mathematics, Shanghai University, Shanghai 200444, China and Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: De-Shuang
authors.initials: DS
authors.lastname: Huang
authors.affiliation: School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, LERIA, University of Angers, 49045 Angers Cedex 01, France, Department of Mathematics, Shanghai University, Shanghai 200444, China and Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Chang-Jun
authors.initials: CJ
authors.lastname: Jiang
authors.affiliation: School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, LERIA, University of Angers, 49045 Angers Cedex 01, France, Department of Mathematics, Shanghai University, Shanghai 200444, China and Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Jin-Kao
authors.initials: JK
authors.lastname: Hao
authors.affiliation: School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, LERIA, University of Angers, 49045 Angers Cedex 01, France, Department of Mathematics, Shanghai University, Shanghai 200444, China and Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Luonan
authors.initials: L
authors.lastname: Chen
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006801:Humans; D035683:MicroRNAs / Q000032:analysis / Q000235:genetics*; D009369:Neoplasms / Q000175:diagnosis / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism
chemical_list: D014408:Biomarkers, Tumor; D035683:MicroRNAs; D012333:RNA, Messenger