title: Large-scale investigation of human TF-miRNA relations based on coexpression profiles.
abstract: Noncoding, endogenous microRNAs (miRNAs) are fairly well known for regulating gene expression rather than protein coding. Dysregulation of miRNA gene, either upregulated or downregulated, may lead to severe diseases or oncogenesis, especially when the miRNA disorder involves significant bioreactions or pathways. Thus, how miRNA genes are transcriptionally regulated has been highlighted as well as target recognition in recent years. In this study, a large-scale investigation of novel cis- and trans-elements was undertaken to further determine TF-miRNA regulatory relations, which are necessary to unravel the transcriptional regulation of miRNA genes. Based on miRNA and annotated gene expression profiles, the term "coTFBS" was introduced to detect common transcription factors and the corresponding binding sites within the promoter regions of each miRNA and its coexpressed annotated genes. The computational pipeline was successfully established to filter redundancy due to short sequence motifs for TFBS pattern search. Eventually, we identified more convinced TF-miRNA regulatory relations for 225 human miRNAs. This valuable information is helpful in understanding miRNA functions and provides knowledge to evaluate the therapeutic potential in clinical research. Once most expression profiles of miRNAs in the latest database are completed, TF candidates of more miRNAs can be explored by this filtering approach in the future.
authors.affiliation: Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Chia-Hung
authors.identifier: 0000-0002-3844-3275
authors.initials: CH
authors.lastname: Chien
authors.affiliation: Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Yi-Fan
authors.initials: YF
authors.lastname: Chiang-Hsieh
authors.affiliation: Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei 112, Taiwan.
authors.forename: Ann-Ping
authors.initials: AP
authors.lastname: Tsou
authors.affiliation: Mackay Medicine, Nursing and Management College, Taipei 112, Taiwan ; Department of Medicine, Mackay Medical College, New Taipei City 252, Taiwan ; Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu 300, Taiwan.
authors.forename: Shun-Long
authors.identifier: 0000-0002-2297-1225
authors.initials: SL
authors.lastname: Weng
authors.affiliation: Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Wen-Chi
authors.identifier: 0000-0002-0347-1516
authors.initials: WC
authors.lastname: Chang
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan ; Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan ; Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 807, Taiwan ; Institute of Biomedical Engineering, National Chiao Tung University, Hsinchu 300, Taiwan.
authors.forename: Hsien-Da
authors.initials: HD
authors.lastname: Huang
mesh_terms: D001665:Binding Sites; D019295:Computational Biology; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D015894:Genome, Human; D006801:Humans; D035683:MicroRNAs / Q000096:biosynthesis* / Q000235:genetics; D058977:Molecular Sequence Annotation; D014157:Transcription Factors / Q000096:biosynthesis* / Q000235:genetics
chemical_list: D035683:MicroRNAs; D014157:Transcription Factors