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Transcriptomic analysis of human endogenous retroviruses in systemic lupus erythematosus.

作者信息

Iñiguez Luis P, de Mulder Rougvie Miguel, Stearrett Nathaniel, Jones Richard B, Ormsby Christopher E, Reyes-Terán Gustavo, Crandall Keith A, Nixon Douglas F, Bendall Matthew L

机构信息

Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021;

Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021.

出版信息

Proc Natl Acad Sci U S A. 2019 Oct 22;116(43):21350-21351. doi: 10.1073/pnas.1907705116. Epub 2019 Oct 8.

DOI:10.1073/pnas.1907705116
PMID:31594853
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6815141/
Abstract
摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/16f7/6815141/4cc03e554bbe/pnas.1907705116fig01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/16f7/6815141/4cc03e554bbe/pnas.1907705116fig01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/16f7/6815141/4cc03e554bbe/pnas.1907705116fig01.jpg

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本文引用的文献

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Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression.望远镜：通过准确估计转座元件的表达来对逆转录组进行特征描述。
PLoS Comput Biol. 2019 Sep 30;15(9):e1006453. doi: 10.1371/journal.pcbi.1006453. eCollection 2019 Sep.
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ERVmap analysis reveals genome-wide transcription of human endogenous retroviruses.ERVmap 分析揭示了人类内源性逆转录病毒的全基因组转录。
Proc Natl Acad Sci U S A. 2018 Dec 11;115(50):12565-12572. doi: 10.1073/pnas.1814589115. Epub 2018 Nov 19.
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A survey of best practices for RNA-seq data analysis.
将人类内源性逆转录病毒整合到转录组全关联研究中，突出了重大精神疾病的新的风险因素。
Nat Commun. 2024 May 22;15(1):3803. doi: 10.1038/s41467-024-48153-z.
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The landscape of hervRNAs transcribed from human endogenous retroviruses across human body sites.人类内源性逆转录病毒在人体不同部位转录的 hervRNA 景观。
Genome Biol. 2022 Nov 3;23(1):231. doi: 10.1186/s13059-022-02804-w.
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HERVs characterize normal and leukemia stem cells and represent a source of shared epitopes for cancer immunotherapy.人类内源性逆转录病毒特征正常和白血病干细胞，并代表癌症免疫治疗的共享表位的来源。
Am J Hematol. 2022 Sep;97(9):1200-1214. doi: 10.1002/ajh.26647. Epub 2022 Jul 12.
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Autoantibodies against the envelope proteins of endogenous retroviruses K102 and K108 in patients with systemic lupus erythematosus correlate with active disease.自身免疫性红斑狼疮患者中针对内源性逆转录病毒 K102 和 K108 包膜蛋白的自身抗体与疾病活动相关。
Clin Exp Rheumatol. 2022 Jul;40(7):1306-1312. doi: 10.55563/clinexprheumatol/2kg1d8. Epub 2021 Oct 13.
7
Expression of Human Endogenous Retroviruses in Systemic Lupus Erythematosus: Multiomic Integration With Gene Expression.人类内源性逆转录病毒在系统性红斑狼疮中的表达：与基因表达的多组学整合。
Front Immunol. 2021 Apr 27;12:661437. doi: 10.3389/fimmu.2021.661437. eCollection 2021.
8
How Retroviruses and Retrotransposons in Our Genome May Contribute to Autoimmunity in Rheumatological Conditions.我们基因组中的逆转录病毒和逆转座子如何导致风湿性疾病中的自身免疫。
Front Immunol. 2020 Nov 13;11:593891. doi: 10.3389/fimmu.2020.593891. eCollection 2020.
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Human Endogenous Retrovirus Expression Is Upregulated in the Breast Cancer Microenvironment of HIV Infected Women: A Pilot Study.人类内源性逆转录病毒在HIV感染女性乳腺癌微环境中表达上调：一项初步研究。
Front Oncol. 2020 Oct 22;10:553983. doi: 10.3389/fonc.2020.553983. eCollection 2020.
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Reply to Iñiguez et al.: ERVmap is a validated approach to mapping proviral endogenous retroviruses in the human genome.回复伊尼格斯等人：ERVmap是一种经过验证的在人类基因组中绘制前病毒内源性逆转录病毒图谱的方法。
Proc Natl Acad Sci U S A. 2019 Oct 22;116(43):21352-21353. doi: 10.1073/pnas.1908504116. Epub 2019 Oct 8.
RNA测序数据分析的最佳实践调查。
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TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets.TE转录本：一个用于在RNA测序数据集差异表达分析中纳入转座元件的软件包。
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Repetitive DNA and next-generation sequencing: computational challenges and solutions.重复 DNA 和新一代测序：计算挑战与解决方案。
Nat Rev Genet. 2011 Nov 29;13(1):36-46. doi: 10.1038/nrg3117.
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RNA-Seq gene expression estimation with read mapping uncertainty.基于读段比对不确定性的 RNA-Seq 基因表达估计。
Bioinformatics. 2010 Feb 15;26(4):493-500. doi: 10.1093/bioinformatics/btp692. Epub 2009 Dec 18.