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

IF 16.6 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Nucleic Acids Research Pub Date : 2024-11-12 DOI:10.1093/nar/gkae1081

Maodi Liang, Chenhao Zhang, Yang Yang, Qinghua Cui, Jun Zhang, Chunmei Cui

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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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TransmiR v3.0：最新转录因子--microRNA调控数据库

microRNA（miRNA）通过介导基因表达活跃于各种生物过程，全面研究miRNA的转录对于了解病理情况下miRNA失调的机制至关重要。本文介绍了更新的 TransmiR v3.0 数据库，其中包含更全面的 miRNA 转录调控信息，包括从 2285 篇论文中筛选出的 5095 条转录因子（TF）-miRNA 调控信息，以及从 ChIP-seq 数据中筛选出的 >600 万条 TF-miRNA 调控信息。目前，TransmiR v3.0 涵盖了 29 种生物的 3260 个 TF、4253 个 miRNA 和 514 433 个 TF-miRNA 调控对。此外，通过对多个物种的 miRNA 启动子序列上的 TF 位点进行主题扫描来预测 TF-miRNA 调控，预测出 284 527 个 TF-miRNA 调控。除了数据量的大幅增长，我们还通过引入 TF 家族、TFBS 主题和多个物种的表达谱，改进了 TF 和 miRNA 的注释。此外，TransmiR v3.0 在线数据库的功能也得到了增强，包括允许批量搜索灵活查询，在 "网络 "模块中提供更广泛的疾病特异性和新的性别特异性 TF-miRNA 调控网络。TransmiR v3.0 为研究 miRNA 生物发生调控提供了有用的资源，可通过 http://www.cuilab.cn/transmir 免费访问。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Nucleic Acids Research 生物-生化与分子生物学

CiteScore

27.10

自引率

4.70%

发文量

1057

审稿时长

2 months

期刊介绍： Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.