dbMTS：一个包含推测的人类 microRNA 靶位点 SNVs 及其功能预测的综合数据库。
dbMTS: A comprehensive database of putative human microRNA target site SNVs and their functional predictions.
机构信息
USF Genomics, College of Public Health, University of South Florida, Tampa, Florida.
Department of Computer Science and Engineering, College of Engineering, University of South Florida, Tampa, Florida.
出版信息
Hum Mutat. 2020 Jun;41(6):1123-1130. doi: 10.1002/humu.24020. Epub 2020 Apr 6.
Abstract
MicroRNAs (miRNA) are short noncoding RNAs that can repress the expression of protein-coding messenger RNAs (mRNAs) by binding to the 3'-untranslated region (UTR) of the target. Genetic mutations such as single nucleotide variants (SNVs) in the 3'-UTR of the mRNAs can disrupt miRNA regulation. In this study, we presented dbMTS, a database for miRNA target site (MTS) SNVs and their functional annotations. This database can help studies easily identify putative SNVs that affect miRNA targeting and facilitate the prioritization of their functional importance. dbMTS is freely available for academic use at http://database.liulab.science/dbMTS as a web service or a downloadable attached database of dbNSFP.
摘要
微小 RNA（miRNA）是短的非编码 RNA，可以通过与靶标 mRNA 的 3'非翻译区（UTR）结合来抑制蛋白质编码信使 RNA（mRNA）的表达。mRNA 的 3'UTR 中的遗传突变，如单核苷酸变异（SNV），可以破坏 miRNA 的调控。在这项研究中，我们提出了 dbMTS，这是一个 miRNA 靶位点（MTS）SNV 及其功能注释的数据库。该数据库可以帮助研究人员轻松识别可能影响 miRNA 靶向的 SNV，并有助于确定其功能重要性的优先级。dbMTS 可在 http://database.liulab.science/dbMTS 上免费供学术使用，作为一个网络服务或 dbNSFP 的可下载附加数据库。
相似文献
1
dbMTS: A comprehensive database of putative human microRNA target site SNVs and their functional predictions.dbMTS：一个包含推测的人类 microRNA 靶位点 SNVs 及其功能预测的综合数据库。
Hum Mutat. 2020 Jun;41(6):1123-1130. doi: 10.1002/humu.24020. Epub 2020 Apr 6.
2
Identification of MicroRNA-Related Tumorigenesis Variants and Genes in the Cancer Genome Atlas (TCGA) Data.在癌症基因组图谱 (TCGA) 数据中识别与肿瘤发生相关的 microRNA 变异体和基因。
Genes (Basel). 2020 Aug 19;11(9):953. doi: 10.3390/genes11090953.
3
Bioinformatics Analysis Revealed Novel 3'UTR Variants Associated with Intellectual Disability.生物信息学分析揭示了与智力障碍相关的新型 3'UTR 变异。
Genes (Basel). 2020 Aug 26;11(9):998. doi: 10.3390/genes11090998.
4
dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs.dbNSFP v4：一个全面的人类非同义突变和剪接位点 SNVs 转录体特异性功能预测和注释数据库。
Genome Med. 2020 Dec 2;12(1):103. doi: 10.1186/s13073-020-00803-9.
5
miRGen 2.0: a database of microRNA genomic information and regulation.miRGen 2.0：一个 miRNA 基因组信息和调控数据库。
Nucleic Acids Res. 2010 Jan;38(Database issue):D137-41. doi: 10.1093/nar/gkp888. Epub 2009 Oct 22.
6
MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets.MicroSNiPer：一个用于预测 SNP 对潜在 miRNA 靶标影响的网络工具。
Hum Mutat. 2010 Nov;31(11):1223-32. doi: 10.1002/humu.21349. Epub 2010 Oct 7.
7
dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations.dbNSFP v2.0：一个人类非同义 SNP 及其功能预测和注释数据库。
Hum Mutat. 2013 Sep;34(9):E2393-402. doi: 10.1002/humu.22376. Epub 2013 Jul 10.
8
dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs.dbNSFP v3.0：一个用于人类非同义突变和剪接位点单核苷酸变异的功能预测与注释一站式数据库。
Hum Mutat. 2016 Mar;37(3):235-41. doi: 10.1002/humu.22932. Epub 2016 Jan 5.
9
Retained introns increase putative microRNA targets within 3' UTRs of human mRNA.保留的内含子增加了人类mRNA 3'UTR内的潜在微小RNA靶标。
FEBS Lett. 2007 Mar 20;581(6):1081-6. doi: 10.1016/j.febslet.2007.02.009. Epub 2007 Feb 14.
10
STarMirDB: A database of microRNA binding sites.STarMirDB：一个微小RNA结合位点数据库。
RNA Biol. 2016 Jun 2;13(6):554-60. doi: 10.1080/15476286.2016.1182279.
引用本文的文献
1
MicroRNA binding site variation is enriched in psychiatric disorders.微小 RNA 结合位点变异在精神疾病中富集。
Hum Mutat. 2022 Dec;43(12):2153-2169. doi: 10.1002/humu.24481. Epub 2022 Oct 23.
2
AntiVIRmiR: A repository of host antiviral miRNAs and their expression along with experimentally validated viral miRNAs and their targets.AntiVIRmiR：宿主抗病毒微小RNA及其表达的储存库，以及经过实验验证的病毒微小RNA及其靶标。
Front Genet. 2022 Sep 8;13:971852. doi: 10.3389/fgene.2022.971852. eCollection 2022.
3
dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs.dbNSFP v4：一个全面的人类非同义突变和剪接位点 SNVs 转录体特异性功能预测和注释数据库。
Genome Med. 2020 Dec 2;12(1):103. doi: 10.1186/s13073-020-00803-9.
4
miRNASNP-v3: a comprehensive database for SNPs and disease-related variations in miRNAs and miRNA targets.miRNASNP-v3：一个综合性的 miRNA 和 miRNA 靶标中 SNPs 和疾病相关变异的数据库。
Nucleic Acids Res. 2021 Jan 8;49(D1):D1276-D1281. doi: 10.1093/nar/gkaa783.
5
Bioinformatics Analysis Revealed Novel 3'UTR Variants Associated with Intellectual Disability.生物信息学分析揭示了与智力障碍相关的新型 3'UTR 变异。
Genes (Basel). 2020 Aug 26;11(9):998. doi: 10.3390/genes11090998.
6
Identification of MicroRNA-Related Tumorigenesis Variants and Genes in the Cancer Genome Atlas (TCGA) Data.在癌症基因组图谱 (TCGA) 数据中识别与肿瘤发生相关的 microRNA 变异体和基因。
Genes (Basel). 2020 Aug 19;11(9):953. doi: 10.3390/genes11090953.
7
The International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019): conference summary and innovations in genomics.2019 年智能生物学与医学国际会议（ICIBM 2019）：会议总结与基因组学创新。
BMC Genomics. 2019 Dec 30;20(Suppl 12):1005. doi: 10.1186/s12864-019-6326-5.
8
QTLbase: an integrative resource for quantitative trait loci across multiple human molecular phenotypes.QTLbase：一个整合的人类分子表型数量性状基因座资源库。
Nucleic Acids Res. 2020 Jan 8;48(D1):D983-D991. doi: 10.1093/nar/gkz888.
本文引用的文献
1
Metazoan MicroRNAs.后生动物 MicroRNAs。
Cell. 2018 Mar 22;173(1):20-51. doi: 10.1016/j.cell.2018.03.006.
2
Genetic variants in microRNA genes and targets associated with cardiovascular disease risk factors in the African-American population.microRNA 基因中的遗传变异及其与非裔美国人心血管疾病风险因素的关联
Hum Genet. 2018 Jan;137(1):85-94. doi: 10.1007/s00439-017-1858-8. Epub 2017 Dec 20.
3
MSDD: a manually curated database of experimentally supported associations among miRNAs, SNPs and human diseases.MSDD：一个手动整理的数据库，其中包含实验支持的 miRNA、SNP 和人类疾病之间的关联。
Nucleic Acids Res. 2018 Jan 4;46(D1):D181-D185. doi: 10.1093/nar/gkx1035.
4
Dissecting the biological relationship between TCGA miRNA and mRNA sequencing data using MMiRNA-Viewer.使用MMiRNA-Viewer剖析TCGA miRNA与mRNA测序数据之间的生物学关系。
BMC Bioinformatics. 2016 Oct 6;17(Suppl 13):336. doi: 10.1186/s12859-016-1219-y.
5
The Ensembl Variant Effect Predictor.Ensembl变异效应预测器。
Genome Biol. 2016 Jun 6;17(1):122. doi: 10.1186/s13059-016-0974-4.
6
Distribution of miRNA expression across human tissues.微小RNA在人体组织中的表达分布。
Nucleic Acids Res. 2016 May 5;44(8):3865-77. doi: 10.1093/nar/gkw116. Epub 2016 Feb 25.
7
A spectral approach integrating functional genomic annotations for coding and noncoding variants.一种整合编码和非编码变异功能基因组注释的光谱方法。
Nat Genet. 2016 Feb;48(2):214-20. doi: 10.1038/ng.3477. Epub 2016 Jan 4.
8
ClinVar: public archive of interpretations of clinically relevant variants.ClinVar：临床相关变异解读的公共存档库。
Nucleic Acids Res. 2016 Jan 4;44(D1):D862-8. doi: 10.1093/nar/gkv1222. Epub 2015 Nov 17.
9
dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs.dbNSFP v3.0：一个用于人类非同义突变和剪接位点单核苷酸变异的功能预测与注释一站式数据库。
Hum Mutat. 2016 Mar;37(3):235-41. doi: 10.1002/humu.22932. Epub 2016 Jan 5.
10
WGSA: an annotation pipeline for human genome sequencing studies.WGSA：一种用于人类基因组测序研究的注释流程。
J Med Genet. 2016 Feb;53(2):111-2. doi: 10.1136/jmedgenet-2015-103423. Epub 2015 Sep 22.
Zotero 插件