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BioMed Research International
Volume 2014 (2014), Article ID 623078, 8 pages
http://dx.doi.org/10.1155/2014/623078
Research Article

Large-Scale Investigation of Human TF-miRNA Relations Based on Coexpression Profiles

1Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
2Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei 112, Taiwan
3Mackay Medicine, Nursing and Management College, Taipei 112, Taiwan
4Department of Medicine, Mackay Medical College, New Taipei City 252, Taiwan
5Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu 300, Taiwan
6Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan
7Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan
8Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
9Institute of Biomedical Engineering, National Chiao Tung University, Hsinchu 300, Taiwan

Received 11 March 2014; Revised 2 May 2014; Accepted 18 May 2014; Published 9 June 2014

Academic Editor: Tzong-Yi Lee

Copyright © 2014 Chia-Hung Chien et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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.