TransmiR v2.0: an updated transcription factor-microRNA regulation database
Open accessAbstract
MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression and play vital roles in various biological processes. It has been reported that aberrant regulation of miRNAs was associated with the development and progression of various diseases, but the underlying mechanisms are not fully deciphered. Here, we described our updated TransmiR v2.0 database for more comprehensive information about transcription factor (TF)-miRNA regulations. 3730 TF-miRNA regulations among 19 species from 1349 reports were manually curated by surveying >8000 publications, and more than 1.7 million tissue-specific TF-miRNA regulations were further incorporated based on ChIP-seq data. Besides, we constructed a 'Predict' module to query the predicted TF-miRNA regulations in human based on binding motifs of TFs. To facilitate the community, we provided a 'Network' module to visualize TF-miRNA regulations for each TF and miRNA, or for a specific disease. An 'Enrichment analysis' module was also included to predict TFs that are likely to regulate a miRNA list of interest. In conclusion, with improved data coverage and webserver functionalities, TransmiR v2.0 would be a useful resource for investigating the regulation of miRNAs. TransmiR v2.0 is freely accessible at http://www.cuilab.cn/transmir.
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According to TransmiR, there is a single ATF1 binding site located in the promoter region of miR-27b-3p.
“According to analysis by TransmiR32, there is a single ATF1 binding site located in the promoter region of miR-27b-3p.”
From ATF1 and miR-27b-3p drive intervertebral disc degeneration through the PPARG/NF-κB signaling axis (2025) · cites this paper as [32]
The Database Construction sections describe how TransmiR identifies putative transcription-factor binding in miRNA promoters, but do not report a result for ATF1 and miR-27b-3p. Searches for those terms found no passage establishing that there is exactly one binding site. (LLM, conf=0.72)
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- Authors
- Tong, Z., Cui, Q., Wang, J., & Zhou, Y.
- Affiliations
- Peking University (CN)
- Corresponding author
- Wang, Juan
- Zhou, Yuan
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-10-29
- Volume
- 47
- Issue
- D1
- Pages
- D253-D258
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC6323981
- OpenAlex
- W2899510892
- Cited by
- 356
- References
- 49
- Citations by year
- 2026: 17 · 2025: 37 · 2024: 56 · 2023: 52 · 2022: 60 · 2021: 66 · 2020: 49 · 2019: 18
- FWCI
- 10.05
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- National Natural Science Foundation of China (81473236)
- Special Project on Precision Medicine under the National Key R&D Program (2016YFC0903000)
- Fundamental Research Funds for Central Universities of China (BMU2017YJ004)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › MicroRNA in disease regulation
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Keywords
- microRNA regulation, transcription factors, post-transcriptional regulation, tissue-specific gene regulation, ChIP-seq, enrichment analysis
- MeSH terms
- Gene Expression Regulation, Humans, Software, Software Design, Transcription Factors, User-Computer Interface, Computational Biology, Genomics, Databases, Genetic, MicroRNAs
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