Detection of cell markers from single cell RNA-seq with sc2marker.
Marker identification
Maximum margin
Single cell RNA-seq
Journal
BMC bioinformatics
ISSN: 1471-2105
Titre abrégé: BMC Bioinformatics
Pays: England
ID NLM: 100965194
Informations de publication
Date de publication:
12 Jul 2022
12 Jul 2022
Historique:
received:
14
01
2022
accepted:
28
06
2022
entrez:
13
7
2022
pubmed:
14
7
2022
medline:
16
7
2022
Statut:
epublish
Résumé
Single-cell RNA sequencing (scRNA-seq) allows the detection of rare cell types in complex tissues. The detection of markers for rare cell types is useful for further biological analysis of, for example, flow cytometry and imaging data sets for either physical isolation or spatial characterization of these cells. However, only a few computational approaches consider the problem of selecting specific marker genes from scRNA-seq data. Here, we propose sc2marker, which is based on the maximum margin index and a database of proteins with antibodies, to select markers for flow cytometry or imaging. We evaluated the performances of sc2marker and competing methods in ranking known markers in scRNA-seq data of immune and stromal cells. The results showed that sc2marker performed better than the competing methods in accuracy, while having a competitive running time.
Sections du résumé
BACKGROUND
BACKGROUND
Single-cell RNA sequencing (scRNA-seq) allows the detection of rare cell types in complex tissues. The detection of markers for rare cell types is useful for further biological analysis of, for example, flow cytometry and imaging data sets for either physical isolation or spatial characterization of these cells. However, only a few computational approaches consider the problem of selecting specific marker genes from scRNA-seq data.
RESULTS
RESULTS
Here, we propose sc2marker, which is based on the maximum margin index and a database of proteins with antibodies, to select markers for flow cytometry or imaging. We evaluated the performances of sc2marker and competing methods in ranking known markers in scRNA-seq data of immune and stromal cells. The results showed that sc2marker performed better than the competing methods in accuracy, while having a competitive running time.
Identifiants
pubmed: 35831796
doi: 10.1186/s12859-022-04817-5
pii: 10.1186/s12859-022-04817-5
pmc: PMC9281170
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
276Subventions
Organisme : Bundesministerium für Bildung und Forschung
ID : Fibromap
Organisme : Deutsche Forschungsgemeinschaft
ID : CRU 344
Informations de copyright
© 2022. The Author(s).
Références
J Biomed Inform. 2015 Feb;53:405-14
pubmed: 25464113
MAbs. 2017 Oct;9(7):1143-1154
pubmed: 28726542
Elife. 2020 Apr 14;9:
pubmed: 32286228
Elife. 2021 Apr 16;10:
pubmed: 33861199
Nat Rev Immunol. 2016 Jul;16(7):449-62
pubmed: 27320317
Cell. 2021 Jun 24;184(13):3573-3587.e29
pubmed: 34062119
Nat Commun. 2021 Feb 17;12(1):1088
pubmed: 33597522
Methods Mol Biol. 2019;1959:247-259
pubmed: 30852827
Genome Biol. 2015 Dec 10;16:278
pubmed: 26653891
Cell Stem Cell. 2021 Apr 1;28(4):637-652.e8
pubmed: 33301706
Nat Methods. 2016 Nov 29;13(12):966-967
pubmed: 27898060
Mol Syst Biol. 2019 Oct;15(10):e9005
pubmed: 31657111
Science. 2015 Jan 23;347(6220):1260419
pubmed: 25613900
Sci Rep. 2017 Mar 30;7:45477
pubmed: 28358118
Genome Biol. 2021 Dec 1;22(1):321
pubmed: 34847932
PLoS One. 2015 Apr 20;10(3):e0121314
pubmed: 25894527
Cell. 2018 Jul 26;174(3):716-729.e27
pubmed: 29961576
Blood. 2012 Jun 7;119(23):5429-37
pubmed: 22553313
Neuroinformatics. 2016 Apr;14(2):169-82
pubmed: 26589523
Nat Commun. 2020 Aug 27;11(1):4307
pubmed: 32855414
Bioinformatics. 2019 Jan 15;35(2):301-308
pubmed: 29931307
Toxicol Appl Pharmacol. 2005 Sep 1;207(2 Suppl):149-51
pubmed: 16153988
Nat Med. 2020 Jul;26(7):1070-1076
pubmed: 32514174
Cell. 2018 Feb 22;172(5):1091-1107.e17
pubmed: 29474909
Cell. 2019 Jun 13;177(7):1888-1902.e21
pubmed: 31178118
Bioinformatics. 2017 Apr 1;33(7):1014-1020
pubmed: 28062447
Nucleic Acids Res. 2021 Jan 8;49(D1):D939-D946
pubmed: 33152070
Nat Cell Biol. 2020 Jan;22(1):38-48
pubmed: 31871321
BMC Bioinformatics. 2020 Oct 23;21(1):477
pubmed: 33097004