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

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

Author information

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/.

PMID:
25932650
PMCID:
PMC4416930
DOI:
10.1371/journal.pone.0125222
[Indexed for MEDLINE]
Free PMC Article

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