TransmiR v3.0: an updated transcription factor-microRNA regulation database

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Abstract

microRNAs (miRNAs) are active in various biological processes by mediating gene expression, and the full investigation of miRNA transcription is crucial for understanding the mechanisms underlying miRNA deregulation in pathological conditions. Here an updated TransmiR v3.0 database is presented with more comprehensive miRNA transcription regulation information, which contains 5095 transcription factor (TF) -miRNA regulations curated from 2285 papers and >6 million TF–miRNA regulations derived from ChIP-seq data. Currently, TransmiR v3.0 covers 3260 TFs, 4253 miRNAs and 514 433 TF–miRNA regulation pairs across 29 organisms. Additionally, motif scanning of TF loci on promoter sequences of miRNAs from multiple species is employed to predict TF–miRNA regulations, generating 284 527 predicted TF–miRNA regulations. Besides the significant growth of data volume, we also improve the annotations for TFs and miRNAs by introducing the TF family, TFBS motif, and expression profiles for several species. Moreover, the functionality of the TransmiR v3.0 online database is enhanced, including allowing batch search for flexible queries and offering more extensive disease-specific, as well as newly sex-specific TF–miRNA regulation networks in the ‘Network’ module. TransmiR v3.0 provides a useful resource for studying miRNA biogenesis regulation and can be freely accessed at http://www.cuilab.cn/transmir.

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Author and article information

Contributors

Maodi Liang

Chenhao Zhang

Yang Yang

Qinghua Cui

Jun Zhang

Chunmei Cui:

ORCID: https://orcid.org/0000-0001-6223-5225

Journal

Journal ID (nlm-ta): Nucleic Acids Res

Journal ID (iso-abbrev): Nucleic Acids Res

Journal ID (publisher-id): nar

Title: Nucleic Acids Research

Publisher: Oxford University Press

ISSN (Print): 0305-1048

ISSN (Electronic): 1362-4962

Publication date Collection: 06 January 2025

Publication date (Electronic): 12 November 2024

Publication date PMC-release: 12 November 2024

Volume: 53

Issue: D1

Pages: D318-D323

Affiliations

School of Sports Medicine, Wuhan Institute of Physical Education , No.461 Luoyu Rd. Wuchang District, WuHan 430079 Hubei Province, China

Department of Biomedical Informatics, Center for Noncoding RNA Medicine, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University , 38 Xueyuan Rd, Beijing 100191, China

Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University Health Science Center , Beijing 100191, China

School of Sports Medicine, Wuhan Institute of Physical Education , No.461 Luoyu Rd. Wuchang District, WuHan 430079 Hubei Province, China

Medical College of Shihezi University, Bei-Er-Lu , Shihezi, Xinjiang 832000, China

Author notes

To whom the correspondence should be addressed. Email: yangsh@ 123456bjmu.edu.cn

Correspondence may also be addressed to Qinghua Cui. Email: cuiqinghua@ 123456bjmu.edu.cn

Correspondence may also be addressed to Jun Zhang. Email: zhangjunyc@ 123456163.com

Correspondence may also be addressed to Chunmei Cui. Tel: +86 10 82801001; Fax: +86 10 82801001; Email: ccm328@ 123456bjmu.edu.cn

The first two authors should be regarded as Joint First Authors.

Author information

Chunmei Cui https://orcid.org/0000-0001-6223-5225

Article

Publisher ID: gkae1081

DOI: 10.1093/nar/gkae1081

PMC ID: 11701595

PubMed ID: 39530226

SO-VID: 1d7ee23f-98c7-4563-86f4-043836936bf3

License:

This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License ( https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact reprints@ 123456oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@ 123456oup.com .

History

Date accepted : 23 October 2024

Date revision received : 21 October 2024

Date received : 05 August 2024

Page count

Pages: 6

Funding

Funded by: National Natural Science Foundation of China, DOI 10.13039/501100001809;

Award ID: 32301239

Award ID: 62025102

Award ID: 81921001

Funded by: Xinjiang Production and Construction Corps, DOI 10.13039/501100009967;

Award ID: 2023AB057

Award ID: 2023ZD037

Award ID: 2022ZD001

Funded by: China Postdoctoral Science Foundation, DOI 10.13039/501100002858;

Award ID: 2023M740151

TransmiR v3.0: an updated transcription factor-microRNA regulation database

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