• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
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
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
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 @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

mirTarRnaSeq：用于 miRNA-mRNA 靶标识别和相互作用分析的 R/Bioconductor 统计软件包。

mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis.

机构信息

Dana Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, United States.

Boston Children's Hospital and Harvard Medical School, Boston, MA, United States.

出版信息

BMC Genomics. 2022 Jun 13;23(1):439. doi: 10.1186/s12864-022-08558-w.

DOI:10.1186/s12864-022-08558-w
PMID:35698050
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9191533/
Abstract

We introduce mirTarRnaSeq, an R/Bioconductor package for quantitative assessment of miRNA-mRNA relationships within sample cohorts. mirTarRnaSeq is a statistical package to explore predicted or pre-hypothesized miRNA-mRNA relationships following target prediction.We present two use cases applying mirTarRnaSeq. First, to identify miRNA targets, we examined EBV miRNAs for interaction with human and virus transcriptomes of stomach adenocarcinoma. This revealed enrichment of mRNA targets highly expressed in CD105+ endothelial cells, monocytes, CD4+ T cells, NK cells, CD19+ B cells, and CD34 cells. Next, to investigate miRNA-mRNA relationships in SARS-CoV-2 (COVID-19) infection across time, we used paired miRNA and RNA sequenced datasets of SARS-CoV-2 infected lung epithelial cells across three time points (4, 12, and 24 hours post-infection). mirTarRnaSeq identified evidence for human miRNAs targeting cytokine signaling and neutrophil regulation immune pathways from 4 to 24 hours after SARS-CoV-2 infection. Confirming the clinical relevance of these predictions, three of the immune specific mRNA-miRNA relationships identified in human lung epithelial cells after SARS-CoV-2 infection were also observed to be differentially expressed in blood from patients with COVID-19. Overall, mirTarRnaSeq is a robust tool that can address a wide-range of biological questions providing improved prediction of miRNA-mRNA interactions.

摘要

我们介绍了 mirTarRnaSeq，这是一个用于在样本队列中定量评估 miRNA-mRNA 关系的 R/Bioconductor 包。mirTarRnaSeq 是一个统计软件包，用于探索基于靶标预测的预测或预先假设的 miRNA-mRNA 关系。我们提出了两个应用 mirTarRnaSeq 的用例。首先，为了识别 miRNA 靶标，我们研究了 EBV miRNAs 与胃腺癌的人类和病毒转录组的相互作用。这揭示了在 CD105+内皮细胞、单核细胞、CD4+T 细胞、NK 细胞、CD19+B 细胞和 CD34 细胞中高度表达的 mRNA 靶标富集。接下来，为了研究 SARS-CoV-2（COVID-19）感染过程中 miRNA-mRNA 关系，我们使用了 SARS-CoV-2 感染肺上皮细胞的配对 miRNA 和 RNA 测序数据集，跨越三个时间点（感染后 4、12 和 24 小时）。mirTarRnaSeq 鉴定了人类 miRNA 靶向细胞因子信号和中性粒细胞调节免疫途径的证据，从 SARS-CoV-2 感染后 4 小时到 24 小时。证实了这些预测的临床相关性，在 SARS-CoV-2 感染后人类肺上皮细胞中鉴定的三个免疫特异性 mRNA-miRNA 关系也在 COVID-19 患者的血液中观察到差异表达。总体而言，mirTarRnaSeq 是一个强大的工具，可以解决广泛的生物学问题，提供 miRNA-mRNA 相互作用的改进预测。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d7d3/9195306/e7d7fbdf3311/12864_2022_8558_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d7d3/9195306/a2c8ca3d978d/12864_2022_8558_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d7d3/9195306/45586cd70dd8/12864_2022_8558_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d7d3/9195306/f9415f908928/12864_2022_8558_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d7d3/9195306/49224d536c89/12864_2022_8558_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d7d3/9195306/e7d7fbdf3311/12864_2022_8558_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d7d3/9195306/a2c8ca3d978d/12864_2022_8558_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d7d3/9195306/45586cd70dd8/12864_2022_8558_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d7d3/9195306/f9415f908928/12864_2022_8558_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d7d3/9195306/49224d536c89/12864_2022_8558_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d7d3/9195306/e7d7fbdf3311/12864_2022_8558_Fig5_HTML.jpg

相似文献

1
mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis.mirTarRnaSeq：用于 miRNA-mRNA 靶标识别和相互作用分析的 R/Bioconductor 统计软件包。
BMC Genomics. 2022 Jun 13;23(1):439. doi: 10.1186/s12864-022-08558-w.
2
SARS-COV-2 as potential microRNA sponge in COVID-19 patients.SARS-CoV-2 作为 COVID-19 患者中的潜在 miRNA 海绵。
BMC Med Genomics. 2022 Apr 23;15(Suppl 2):94. doi: 10.1186/s12920-022-01243-7.
3
Contribution of Host miRNA-223-3p to SARS-CoV-Induced Lung Inflammatory Pathology.宿主 miRNA-223-3p 对 SARS-CoV 诱导的肺部炎症病理的贡献。
mBio. 2022 Apr 26;13(2):e0313521. doi: 10.1128/mbio.03135-21. Epub 2022 Mar 1.
4
Gene signatures and potential therapeutic targets of Middle East respiratory syndrome coronavirus (MERS-CoV)-infected human lung adenocarcinoma epithelial cells.中东呼吸综合征冠状病毒（MERS-CoV）感染人肺腺癌细胞的基因特征和潜在治疗靶点。
J Microbiol Immunol Infect. 2021 Oct;54(5):845-857. doi: 10.1016/j.jmii.2021.03.007. Epub 2021 Mar 26.
5
The role of microRNAs in modulating SARS-CoV-2 infection in human cells: a systematic review.microRNAs 在调节人类细胞中 SARS-CoV-2 感染中的作用：系统评价。
Infect Genet Evol. 2021 Jul;91:104832. doi: 10.1016/j.meegid.2021.104832. Epub 2021 Apr 1.
6
A new insight into sex-specific non-coding RNAs and networks in response to SARS-CoV-2.对 SARS-CoV-2 反应中性别特异性非编码 RNA 及网络的新认识。
Infect Genet Evol. 2022 Jan;97:105195. doi: 10.1016/j.meegid.2021.105195. Epub 2021 Dec 23.
7
Role of SARS-CoV-2 in Altering the RNA-Binding Protein and miRNA-Directed Post-Transcriptional Regulatory Networks in Humans.SARS-CoV-2 在改变人类 RNA 结合蛋白和 miRNA 靶向的转录后调控网络中的作用。
Int J Mol Sci. 2020 Sep 25;21(19):7090. doi: 10.3390/ijms21197090.
8
Deciphering the link between Diabetes mellitus and SARS-CoV-2 infection through differential targeting of microRNAs in the human pancreas.通过对人胰腺中 microRNAs 的差异靶向作用来破译糖尿病与 SARS-CoV-2 感染之间的联系。
J Endocrinol Invest. 2022 Mar;45(3):537-550. doi: 10.1007/s40618-021-01693-3. Epub 2021 Oct 20.
9
Identification of potential miRNA-mRNA regulatory network contributing to pathogenesis of HBV-related HCC.鉴定参与 HBV 相关 HCC 发病机制的潜在 miRNA-mRNA 调控网络。
J Transl Med. 2019 Jan 3;17(1):7. doi: 10.1186/s12967-018-1761-7.
10
Expression profiling of human immune cell subsets identifies miRNA-mRNA regulatory relationships correlated with cell type specific expression.鉴定人类免疫细胞亚群的表达谱，确定与细胞类型特异性表达相关的 miRNA-mRNA 调控关系。
PLoS One. 2012;7(1):e29979. doi: 10.1371/journal.pone.0029979. Epub 2012 Jan 20.

引用本文的文献

1
Non-Coding RNAs and Immune Evasion in Human Gamma-Herpesviruses.人类γ-疱疹病毒中的非编码RNA与免疫逃逸
Viruses. 2025 Jul 17;17(7):1006. doi: 10.3390/v17071006.
2
Advancing miRNA cancer research through artificial intelligence: from biomarker discovery to therapeutic targeting.通过人工智能推进微小RNA癌症研究：从生物标志物发现到治疗靶点
Med Oncol. 2024 Dec 17;42(1):30. doi: 10.1007/s12032-024-02579-z.
3
Osteoclast-Derived Exosomal miR-5134-5p Interferes with Alveolar Bone Homeostasis by Targeting the JAK2/STAT3 Axis.破骨细胞衍生的外泌体 miR-5134-5p 通过靶向 JAK2/STAT3 轴干扰牙槽骨稳态。

本文引用的文献

1
Rethinking immunology.重新思考免疫学。
Science. 2021 Jul 16;373(6552):276-277. doi: 10.1126/science.abj5637.
2
Galectin-9, a Player in Cytokine Release Syndrome and a Surrogate Diagnostic Biomarker in SARS-CoV-2 Infection.半乳糖凝集素 9：细胞因子释放综合征的参与者和 SARS-CoV-2 感染的替代诊断生物标志物。
mBio. 2021 May 4;12(3):e00384-21. doi: 10.1128/mBio.00384-21.
3
In-vitro acetylation of SARS-CoV and SARS-CoV-2 nucleocapsid proteins by human PCAF and GCN5.人类 PCAF 和 GCN5 对 SARS-CoV 和 SARS-CoV-2 核衣壳蛋白的体外乙酰化作用。
Int J Nanomedicine. 2023 Jul 7;18:3727-3744. doi: 10.2147/IJN.S413692. eCollection 2023.
4
Identifying Key Regulators of Keratinization in Lung Squamous Cell Cancer Using Integrated TCGA Analysis.利用整合的TCGA分析鉴定肺鳞状细胞癌中角质化的关键调节因子
Cancers (Basel). 2023 Mar 30;15(7):2066. doi: 10.3390/cancers15072066.
5
RNA-seq and microRNA association analysis to explore the pathogenic mechanism of DHAV-1 infection with DEHs.RNA-seq 和 microRNA 关联分析探索 DEHs 中 DHAV-1 感染的致病机制。
Funct Integr Genomics. 2023 Mar 23;23(2):99. doi: 10.1007/s10142-023-01022-2.
Biochem Biophys Res Commun. 2021 Jun 11;557:273-279. doi: 10.1016/j.bbrc.2021.03.173. Epub 2021 Apr 8.
4
Identification of Targeted Pathogenic Markers in Acute Myeloid Leukemia through Integrative Bioinformatics Analysis and Clinical Validation.通过整合生物信息学分析和临床验证鉴定急性髓系白血病中的靶向致病标志物
J Oncol. 2021 Mar 19;2021:5531736. doi: 10.1155/2021/5531736. eCollection 2021.
5
Longitudinal profiling of respiratory and systemic immune responses reveals myeloid cell-driven lung inflammation in severe COVID-19.严重 COVID-19 患者肺部炎症由髓系细胞驱动的呼吸道和全身免疫反应纵向分析。
Immunity. 2021 Apr 13;54(4):797-814.e6. doi: 10.1016/j.immuni.2021.03.005. Epub 2021 Mar 11.
6
COVID-19 and the human innate immune system.新型冠状病毒肺炎与人类固有免疫系统。
Cell. 2021 Apr 1;184(7):1671-1692. doi: 10.1016/j.cell.2021.02.029. Epub 2021 Feb 16.
7
Interleukin-1 and interleukin-6 inhibition compared with standard management in patients with COVID-19 and hyperinflammation: a cohort study.白细胞介素-1和白细胞介素-6抑制与COVID-19合并高炎症患者标准治疗的比较：一项队列研究
Lancet Rheumatol. 2021 Apr;3(4):e253-e261. doi: 10.1016/S2665-9913(21)00012-6. Epub 2021 Feb 3.
8
The Gene Expression Deconvolution Interactive Tool (GEDIT): accurate cell type quantification from gene expression data.基因表达去卷积交互工具（GEDIT）：从基因表达数据中准确量化细胞类型。
Gigascience. 2021 Feb 16;10(2). doi: 10.1093/gigascience/giab002.
9
Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy.对感染SARS-CoV-2的人类细胞系进行转录组分析确定HSP90为COVID-19治疗靶点。
iScience. 2021 Mar 19;24(3):102151. doi: 10.1016/j.isci.2021.102151. Epub 2021 Feb 6.
10
Computationally predicted SARS-COV-2 encoded microRNAs target NFKB, JAK/STAT and TGFB signaling pathways.通过计算预测，严重急性呼吸综合征冠状病毒2（SARS-COV-2）编码的微小RNA靶向核因子κB（NFKB）、Janus激酶/信号转导和转录激活因子（JAK/STAT）以及转化生长因子β（TGFB）信号通路。
Gene Rep. 2021 Mar;22:101012. doi: 10.1016/j.genrep.2020.101012. Epub 2020 Dec 31.