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.

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

Grant support

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.