دورية أكاديمية
أعرض في EDS

Single-cell Mayo Map (scMayoMap): an easy-to-use tool for cell type annotation in single-cell RNA-sequencing data analysis.

التفاصيل البيبلوغرافية
العنوان: Single-cell Mayo Map (scMayoMap): an easy-to-use tool for cell type annotation in single-cell RNA-sequencing data analysis.
المؤلفون: Yang L; Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA.; Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA., Ng YE; Robert and Arlene Kogod Center On Aging, Mayo Clinic, Rochester, MN, 55905, USA., Sun H; Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA., Li Y; Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA., Chini LCS; Robert and Arlene Kogod Center On Aging, Mayo Clinic, Rochester, MN, 55905, USA., LeBrasseur NK; Robert and Arlene Kogod Center On Aging, Mayo Clinic, Rochester, MN, 55905, USA. lebrasseur.nathan@mayo.edu.; Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, 55905, USA. lebrasseur.nathan@mayo.edu., Chen J; Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA. chen.jun2@mayo.edu.; Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA. chen.jun2@mayo.edu., Zhang X; Robert and Arlene Kogod Center On Aging, Mayo Clinic, Rochester, MN, 55905, USA. zhang.xu@mayo.edu.; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA. zhang.xu@mayo.edu.
المصدر: BMC biology [BMC Biol] 2023 Oct 20; Vol. 21 (1), pp. 223. Date of Electronic Publication: 2023 Oct 20.
نوع المنشور: Journal Article; Research Support, U.S. Gov't, Non-P.H.S.; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: BioMed Central Country of Publication: England NLM ID: 101190720 Publication Model: Electronic Cited Medium: Internet ISSN: 1741-7007 (Electronic) Linking ISSN: 17417007 NLM ISO Abbreviation: BMC Biol Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [London] : BioMed Central, c2003-
مواضيع طبية MeSH: Software* , Single-Cell Analysis*/methods, Data Analysis ; RNA ; Sequence Analysis, RNA/methods ; Gene Expression Profiling/methods
مستخلص: Background: Single-cell RNA-sequencing (scRNA-seq) has become a widely used tool for both basic and translational biomedical research. In scRNA-seq data analysis, cell type annotation is an essential but challenging step. In the past few years, several annotation tools have been developed. These methods require either labeled training/reference datasets, which are not always available, or a list of predefined cell subset markers, which are subject to biases. Thus, a user-friendly and precise annotation tool is still critically needed.
Results: We curated a comprehensive cell marker database named scMayoMapDatabase and developed a companion R package scMayoMap, an easy-to-use single-cell annotation tool, to provide fast and accurate cell type annotation. The effectiveness of scMayoMap was demonstrated in 48 independent scRNA-seq datasets across different platforms and tissues. Additionally, the scMayoMapDatabase can be integrated with other tools and further improve their performance.
Conclusions: scMayoMap and scMayoMapDatabase will help investigators to define the cell types in their scRNA-seq data in a streamlined and user-friendly way.
(© 2023. BioMed Central Ltd., part of Springer Nature.)
التعليقات: Update of: bioRxiv. 2023 May 04;:. (PMID: 37205463)
References: Nat Commun. 2022 Sep 27;13(1):5671. (PMID: 36167854)
Cell Syst. 2019 Aug 28;9(2):207-213.e2. (PMID: 31377170)
Nat Aging. 2022 Jul;2(7):601-615. (PMID: 36147777)
Cell. 2021 Jun 24;184(13):3573-3587.e29. (PMID: 34062119)
Genome Biol. 2019 Sep 9;20(1):194. (PMID: 31500660)
iScience. 2020 Mar 27;23(3):100882. (PMID: 32062421)
Cell Syst. 2016 Oct 26;3(4):385-394.e3. (PMID: 27693023)
Cell. 2018 Feb 22;172(5):1091-1107.e17. (PMID: 29474909)
Nature. 2018 Oct;562(7727):367-372. (PMID: 30283141)
BMC Biol. 2023 Oct 20;21(1):223. (PMID: 37858214)
Nat Methods. 2019 Oct;16(10):1007-1015. (PMID: 31501550)
Genome Biol. 2019 Nov 19;20(1):242. (PMID: 31744515)
Nat Immunol. 2019 Feb;20(2):163-172. (PMID: 30643263)
Nucleic Acids Res. 2019 Jan 8;47(D1):D801-D806. (PMID: 30407599)
Database (Oxford). 2010 Aug 05;2010:baq020. (PMID: 20689021)
Front Genet. 2020 May 12;11:490. (PMID: 32477414)
Database (Oxford). 2019 Jan 1;2019:. (PMID: 30951143)
Cell Syst. 2016 Oct 26;3(4):346-360.e4. (PMID: 27667365)
Cell Metab. 2016 Oct 11;24(4):608-615. (PMID: 27667665)
Nucleic Acids Res. 2019 Jan 8;47(D1):D900-D908. (PMID: 30329142)
Commun Biol. 2023 May 20;6(1):545. (PMID: 37210444)
Nat Commun. 2021 Feb 15;12(1):1029. (PMID: 33589635)
Nat Methods. 2018 May;15(5):359-362. (PMID: 29608555)
Cells. 2022 Dec 22;12(1):. (PMID: 36611841)
Cell. 2018 May 3;173(4):879-893.e13. (PMID: 29681456)
Nucleic Acids Res. 2019 Jan 8;47(D1):D721-D728. (PMID: 30289549)
Nat Med. 2018 Jul;24(7):978-985. (PMID: 29942094)
Nat Biotechnol. 2020 Jun;38(6):737-746. (PMID: 32341560)
Genes (Basel). 2019 Jul 12;10(7):. (PMID: 31336988)
Cell Metab. 2016 Oct 11;24(4):593-607. (PMID: 27667667)
معلومات مُعتمدة: R21 HG011662 United States HG NHGRI NIH HHS; U54 AG079754 United States AG NIA NIH HHS; U54 AG044170 United States AG NIA NIH HHS; P01 AG062413 United States AG NIA NIH HHS; R01 GM144351 United States GM NIGMS NIH HHS; R01 AG055529 United States AG NIA NIH HHS
فهرسة مساهمة: Keywords: Cell type annotation; Cell type markers; Single-cell RNA-sequencing; scMayoMap; scMayoMapDatabase
المشرفين على المادة: 63231-63-0 (RNA)
تواريخ الأحداث: Date Created: 20231020 Date Completed: 20231023 Latest Revision: 20240210
رمز التحديث: 20240210
مُعرف محوري في PubMed: PMC10588107
DOI: 10.1186/s12915-023-01728-6
PMID: 37858214
قاعدة البيانات: MEDLINE
الوصف
تدمد:1741-7007
DOI:10.1186/s12915-023-01728-6