TMREC: A Database of Transcription Factor and MiRNA Regulatory Cascades in Human Diseases

Shuyuan Wang; Wei Li; Baofeng Lian; Xinyi Liu; Yan Zhang; Enyu Dai; Xuexin Yu; Fanlin Meng; Wei Jiang; Xia Li

doi:10.1371/journal.pone.0125222

TMREC: A Database of Transcription Factor and MiRNA Regulatory Cascades in Human Diseases

PLoS One. 2015 May 1;10(5):e0125222. doi: 10.1371/journal.pone.0125222. eCollection 2015.

Authors

Shuyuan Wang¹, Wei Li², Baofeng Lian³, Xinyi Liu¹, Yan Zhang¹, Enyu Dai¹, Xuexin Yu¹, Fanlin Meng¹, Wei Jiang¹, Xia Li¹

Affiliations

¹ College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P. R. China.
² College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P. R. China; EpiRNA Lab, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, P. R. China.
³ College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P. R. China; School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China; Shanghai Center for Bioinformation Technology, Shanghai, 201203, P. R. China.

Abstract

Over the past decades, studies have reported that the combinatorial regulation of transcription factors (TFs) and microRNAs (miRNAs) is essential for the appropriate execution of biological events and developmental processes. Dysregulations of these regulators often cause diseases. However, there are no available resources on the regulatory cascades of TFs and miRNAs in the context of human diseases. To fulfill this vacancy, we established the TMREC database in this study. First, we integrated curated transcriptional and post-transcriptional regulations to construct the TF and miRNA regulatory network. Next, we identified all linear paths using the Breadth First Search traversal method. Finally, we used known disease-related genes and miRNAs to measure the strength of association between cascades and diseases. Currently, TMREC consists of 74,248 cascades and 25,194 cascade clusters, involving in 412 TFs, 266 miRNAs and 545 diseases. With the expanding of experimental support regulation data, we will regularly update the database. TMREC aims to help experimental biologists to comprehensively analyse gene expression regulation, to understand the aetiology and to predict novel therapeutic targets. TMREC is freely available at http://bioinfo.hrbmu.edu.cn/TMREC/.

Publication types

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

MeSH terms

Algorithms
Cluster Analysis
Databases, Genetic*
Disease / genetics*
Gene Regulatory Networks*
Humans
MicroRNAs / genetics*
Transcription Factors / metabolism*
User-Computer Interface

Substances

MicroRNAs
Transcription Factors

Grants and funding

This work was supported by the Funds for the Graduate Innovation Fund of Heilongjiang Province (YJSCX2012-250HLJ), the Creative Research Groups of The National Natural Science Foundation of China (81121003), the National Natural Science Foundation of China (30900837, 61170154 and 81202074), the Program for Young Talents of Science and Technology in Harbin (2013RFQXJ057), the Heilong Jiang Postdoctoral Funds for Scientific Research Initiation (LBH-Q11042). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.