Investigating microRNA-target interaction-supported tissues in human cancer tissues based on miRNA and target gene expression profiling

Wan J Hsieh; Feng-Mao Lin; Hsien-Da Huang; Hsiuying Wang

doi:10.1371/journal.pone.0095697

Investigating microRNA-target interaction-supported tissues in human cancer tissues based on miRNA and target gene expression profiling

PLoS One. 2014 Apr 22;9(4):e95697. doi: 10.1371/journal.pone.0095697. eCollection 2014.

Authors

Wan J Hsieh¹, Feng-Mao Lin², Hsien-Da Huang², Hsiuying Wang¹

Affiliations

¹ Institute of Statistics, National Chiao Tung University, Hsinchu, Taiwan.
² Department of Biological Science and Technology, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.

Abstract

Recent studies have revealed that a small non-coding RNA, microRNA (miRNA) down-regulates its mRNA targets. This effect is regarded as an important role in various biological processes. Many studies have been devoted to predicting miRNA-target interactions. These studies indicate that the interactions may only be functional in some specific tissues, which depend on the characteristics of an miRNA. No systematic methods have been established in the literature to investigate the correlation between miRNA-target interactions and tissue specificity through microarray data. In this study, we propose a method to investigate miRNA-target interaction-supported tissues, which is based on experimentally validated miRNA-target interactions. The tissue specificity results by our method are in accordance with the experimental results in the literature.

Availability and implementation: Our analysis results are available at http://tsmti.mbc.nctu.edu.tw/ and http://www.stat.nctu.edu.tw/hwang/tsmti.html.

Publication types

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

MeSH terms

Algorithms
Cluster Analysis
Computational Biology / methods
Databases, Nucleic Acid
Gene Expression Profiling*
Gene Expression Regulation, Neoplastic*
Humans
Internet
MicroRNAs / genetics*
Neoplasms / genetics*
RNA Interference*
RNA, Messenger / genetics*
Tissue Banks

Substances

MicroRNAs
RNA, Messenger

Grants and funding

The authors would like to thank the National Science Council of the Republic of China for financially supporting this research under Contract No. NSC 98-2311-B-009-004-MY3, NSC 99-2627-B-009-003, NSC 101-2311-B-009-003-MY3, NSC 100-2627-B-009-002, NSC 101-2118-M-009-006-MY2, NSC 101-2811-M-009-064 and NSC 102-2911-I-009-101. This work was supported in part by the UST-UCSD International Center of Excellence in Advanced Bio-engineering sponsored by the Taiwan National Science Council I-RiCE Program under Grant Number: NSC 101-2911-I-009-101, and Veterans General Hospitals and University System of Taiwan (VGHUST) Joint Research Program under Grant Number: VGHUST101-G5-1-1 and VGHUST103-G5-1-2. This work was also partially supported by MOE ATU and National Center for Theoretical Sciences. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.