文献检索文档翻译深度研究
Suppr Zotero 插件Zotero 插件
邀请有礼套餐&价格历史记录

新学期，新优惠

限时优惠:9月1日-9月22日

30天高级会员仅需29元

1天体验卡首发特惠仅需5.99元

了解详情
不再提醒
插件&应用
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
高级版
套餐订阅购买积分包
AI 工具
文献检索文档翻译深度研究
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2025

mirTrans：人类细胞系中 microRNAs 转录调控的资源。

mirTrans: a resource of transcriptional regulation on microRNAs for human cell lines.

机构信息

The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Science, Nanjing University, Nanjing 210023, China.

Institute of Bioinformatics, University Medical Center Goettingen, Goldschmidtstrasse 1, D-37077 Goettingen, Germany.

出版信息

Nucleic Acids Res. 2018 Jan 4;46(D1):D168-D174. doi: 10.1093/nar/gkx996.

DOI:10.1093/nar/gkx996
PMID:29077896
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5753250/
Abstract

The cell-specific information of transcriptional regulation on microRNAs (miRNAs) is crucial to the precise understanding of gene regulations in various physiological and pathological processes existed in different tissues and cell types. The database, mirTrans, provides comprehensive information about cell-specific transcription of miRNAs including the transcriptional start sites (TSSs) of miRNAs, transcription factor (TF) to miRNA regulations and miRNA promoter sequences. mirTrans also maps the experimental H3K4me3 and DHS (DNase-I hypersensitive site) marks within miRNA promoters and expressed sequence tags (ESTs) within transcribed regions. The current version of database covers 35 259 TSSs and over 2.3 million TF-miRNA regulations for 1513 miRNAs in a total of 54 human cell lines. These cell lines span most of the biological systems, including circulatory system, digestive system and nervous system. Information for both the intragenic miRNAs and intergenic miRNAs is offered. Particularly, the quality of miRNA TSSs and TF-miRNA regulations is evaluated by literature curation. 23 447 TSS records and 2148 TF-miRNA regulations are supported by special experiments as a result of literature curation. EST coverage is also used to evaluate the accuracy of miRNA TSSs. Interface of mirTrans is friendly designed and convenient to make downloads (http://mcube.nju.edu.cn/jwang/lab/soft/mirtrans/ or http://120.27.239.192/mirtrans/).

摘要

miRNA 转录调控的细胞特异性信息对于精确理解不同组织和细胞类型中存在的各种生理和病理过程中的基因调控至关重要。mirTrans 数据库提供了有关 miRNA 细胞特异性转录的综合信息，包括 miRNA 的转录起始位点（TSS）、转录因子（TF）到 miRNA 的调控以及 miRNA 启动子序列。mirTrans 还绘制了 miRNA 启动子内的实验 H3K4me3 和 DHS（DNase-I 超敏位点）标记以及转录区域内的表达序列标签（EST）。该数据库的当前版本涵盖了 54 个人类细胞系中 1513 个 miRNA 的 35259 个 TSS 和超过 230 万个 TF-miRNA 调控。这些细胞系涵盖了大多数生物系统，包括循环系统、消化系统和神经系统。提供了内含子 miRNA 和基因间 miRNA 的信息。特别是，miRNA TSS 和 TF-miRNA 调控的质量通过文献整理进行评估。由于文献整理，有 23447 个 TSS 记录和 2148 个 TF-miRNA 调控得到了特殊实验的支持。EST 覆盖度也用于评估 miRNA TSS 的准确性。mirTrans 的界面设计友好，便于下载（http://mcube.nju.edu.cn/jwang/lab/soft/mirtrans/ 或 http://120.27.239.192/mirtrans/）。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5f27/5753250/e74e4b0863c0/gkx996fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5f27/5753250/9c185c9aa45e/gkx996fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5f27/5753250/760c91fa845b/gkx996fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5f27/5753250/e74e4b0863c0/gkx996fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5f27/5753250/9c185c9aa45e/gkx996fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5f27/5753250/760c91fa845b/gkx996fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5f27/5753250/e74e4b0863c0/gkx996fig3.jpg

相似文献

[1]
mirTrans: a resource of transcriptional regulation on microRNAs for human cell lines.

Nucleic Acids Res. 2018-1-4

[2]
Identifying cell-specific microRNA transcriptional start sites.

Bioinformatics. 2016-4-19

[3]
Identification of active miRNA promoters from nuclear run-on RNA sequencing.

Nucleic Acids Res. 2017-7-27

[4]
DIANA-miRGen v4: indexing promoters and regulators for more than 1500 microRNAs.

Nucleic Acids Res. 2021-1-8

[5]
Identifying Pri-miRNA Transcription Start Sites.

Methods Mol Biol. 2018

[6]
DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators.

Nucleic Acids Res. 2016-1-4

[7]
Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data.

Nucleic Acids Res. 2011-8-5

[8]
TransmiR v2.0: an updated transcription factor-microRNA regulation database.

Nucleic Acids Res. 2019-1-8

[9]
miRT: a database of validated transcription start sites of human microRNAs.

Genomics Proteomics Bioinformatics. 2012-9-29

[10]
MicroRNA transcription start site prediction with multi-objective feature selection.

Stat Appl Genet Mol Biol. 2012-1-6

引用本文的文献

[1]
The Abnormal ERα-miRNA Cross-Talk in AD-Affected Human Hippocampus: A Bioinformatics Perspective.

Mol Neurobiol. 2025-6

[2]
miRStart 2.0: enhancing miRNA regulatory insights through deep learning-based TSS identification.

Nucleic Acids Res. 2025-1-6

[3]
TransmiR v3.0: an updated transcription factor-microRNA regulation database.

Nucleic Acids Res. 2025-1-6

[4]
Global-local aware Heterogeneous Graph Contrastive Learning for multifaceted association prediction in miRNA-gene-disease networks.

Brief Bioinform. 2024-7-25

[5]
BAP31-Mediated miR-206/133b Cluster Promotes Transendothelial Migration and Metastasis of Colorectal Cancer.

Int J Mol Sci. 2023-11-25

[6]
Comparative Analysis of Published Database Predicting MicroRNA Binding in 3'UTR of mRNA in Diverse Species.

Microrna. 2024

[7]
Circulating MicroRNAs as Cancer Biomarkers in Liquid Biopsies.

Adv Exp Med Biol. 2022

[8]
TRmir: A Comprehensive Resource for Human Transcriptional Regulatory Information of MiRNAs.

Front Genet. 2022-2-4

[9]
MicroRNA expression is deregulated by aberrant methylation in B-cell acute lymphoblastic leukemia mouse model.

Mol Biol Rep. 2022-3

[10]
Transcription Factors and Methylation Drive Prognostic miRNA Dysregulation in Hepatocellular Carcinoma.

Front Oncol. 2021-7-1

本文引用的文献

[1]
An integrated expression atlas of miRNAs and their promoters in human and mouse.

Nat Biotechnol. 2017-9

[2]
Identification of active miRNA promoters from nuclear run-on RNA sequencing.

Nucleic Acids Res. 2017-7-27

[3]
MicroRNA therapeutics: towards a new era for the management of cancer and other diseases.

Nat Rev Drug Discov. 2017-2-17

[4]
ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data.

Nucleic Acids Res. 2017-1-4

[5]
Identifying cell-specific microRNA transcriptional start sites.

Bioinformatics. 2016-4-19

[6]
DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators.

Nucleic Acids Res. 2016-1-4

[7]
Identification of potential biomarkers to differentially diagnose solid pseudopapillary tumors and pancreatic malignancies via a gene regulatory network.

J Transl Med. 2015-11-14

[8]
The NF-κB p65/miR-23a-27a-24 cluster is a target for leukemia treatment.

Oncotarget. 2015-10-20

[9]
Determining the role of microRNAs in psychiatric disorders.

Nat Rev Neurosci. 2015-4

[10]
microTSS: accurate microRNA transcription start site identification reveals a significant number of divergent pri-miRNAs.

Nat Commun. 2014-12-10

文献AI研究员

20分钟写一篇综述，助力文献阅读效率提升50倍

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

推荐工具

医学文档翻译智能文献检索