TransmiR v2.0: an updated transcription factor-microRNA regulation database

By Zhan Tong, Qinghua Cui, Juan Wang, Yuan Zhou. Nucleic Acids Res., 2018

302 citations recorded by the source corpus.

Abstract 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.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/862930bd81b4a40520b8ab1e1b7c7ef4f094d7a0

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In Cancer Research

1. Jianguo Xia
2. Le Chang
3. Guangyan Zhou
4. Othman Soufan

In Molecular Biology

1. Guangyan Zhou
2. Othman Soufan
3. Le Chang
4. Jianguo Xia
5. David S. Wishart
6. Jasmine Chong
7. Igor Sinelnikov

Citations in the corpus

• miRNet 2.0: network-based visual analytics for miRNA functional analysis and systems biology (2020, methodology): “The interactions among miRNAs, TFs and genes are obtained from TransmiR 2.0 (30), ENCODE (31), JASPAR (32) and ChEA (33).”
• miRTarBase update 2022: an informative resource for experimentally validated miRNA–target interactions (2021, methodology): “0 (32), miRSponge 2015 (33) miRNA expression TissueAtlas 2016 (12), EVmiRNA 2019 (13), GEO”
• miRTarBase 2020: updates to the experimentally validated microRNA–target interaction database (2019, methodology): “List of the databases that are integrated by miRTarBase Type Database name Gene and miRNA-specific databases miRBase (7), NCBI Entrez gene (29), NCBI RefSeq (30) SNP or mutation related databases SomamiR (22,31) miRNA–disease association Database HMDD (9,10) The regulation of miRNAs TransMir (19), m”