Cell type identification from single-cell transcriptomes in melanoma

Abstract Background Single-cell sequencing approaches allow gene expression to be measured at the single-cell level, providing opportunities and challenges to study the aetiology of complex diseases, including cancer. Methods Based on single-cell gene and lncRNA expression levels, we proposed a comp...

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Autores principales:	Qiuyan Huo, Yu Yin, Fangfang Liu, Yuying Ma, Liming Wang, Guimin Qin
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Single-cell sequencing Melanoma Cell type Cell marker lncRNA Internal medicine RC31-1245 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/376d7da8df7b4c7ba77f56a0d0d526ba
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spelling	oai:doaj.org-article:376d7da8df7b4c7ba77f56a0d0d526ba2021-11-21T12:04:17ZCell type identification from single-cell transcriptomes in melanoma10.1186/s12920-021-01118-31755-8794https://doaj.org/article/376d7da8df7b4c7ba77f56a0d0d526ba2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12920-021-01118-3https://doaj.org/toc/1755-8794Abstract Background Single-cell sequencing approaches allow gene expression to be measured at the single-cell level, providing opportunities and challenges to study the aetiology of complex diseases, including cancer. Methods Based on single-cell gene and lncRNA expression levels, we proposed a computational framework for cell type identification that fully considers cell dropout characteristics. First, we defined the dropout features of the cells and identified the dropout clusters. Second, we constructed a differential co-expression network and identified differential modules. Finally, we identified cell types based on the differential modules. Results The method was applied to single-cell melanoma data, and eight cell types were identified. Enrichment analysis of the candidate cell marker genes for the two key cell types showed that both key cell types were closely related to the physiological activities of the major histocompatibility complex (MHC); one key cell type was associated with mitosis-related activities, and the other with pathways related to ten diseases. Conclusions Through identification and analysis of key melanoma-related cell types, we explored the molecular mechanism of melanoma, providing insight into melanoma research. Moreover, the candidate cell markers for the two key cell types are potential therapeutic targets for melanoma.Qiuyan HuoYu YinFangfang LiuYuying MaLiming WangGuimin QinBMCarticleSingle-cell sequencingMelanomaCell typeCell markerlncRNAInternal medicineRC31-1245GeneticsQH426-470ENBMC Medical Genomics, Vol 14, Iss S5, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Single-cell sequencing Melanoma Cell type Cell marker lncRNA Internal medicine RC31-1245 Genetics QH426-470
spellingShingle	Single-cell sequencing Melanoma Cell type Cell marker lncRNA Internal medicine RC31-1245 Genetics QH426-470 Qiuyan Huo Yu Yin Fangfang Liu Yuying Ma Liming Wang Guimin Qin Cell type identification from single-cell transcriptomes in melanoma
description	Abstract Background Single-cell sequencing approaches allow gene expression to be measured at the single-cell level, providing opportunities and challenges to study the aetiology of complex diseases, including cancer. Methods Based on single-cell gene and lncRNA expression levels, we proposed a computational framework for cell type identification that fully considers cell dropout characteristics. First, we defined the dropout features of the cells and identified the dropout clusters. Second, we constructed a differential co-expression network and identified differential modules. Finally, we identified cell types based on the differential modules. Results The method was applied to single-cell melanoma data, and eight cell types were identified. Enrichment analysis of the candidate cell marker genes for the two key cell types showed that both key cell types were closely related to the physiological activities of the major histocompatibility complex (MHC); one key cell type was associated with mitosis-related activities, and the other with pathways related to ten diseases. Conclusions Through identification and analysis of key melanoma-related cell types, we explored the molecular mechanism of melanoma, providing insight into melanoma research. Moreover, the candidate cell markers for the two key cell types are potential therapeutic targets for melanoma.
format	article
author	Qiuyan Huo Yu Yin Fangfang Liu Yuying Ma Liming Wang Guimin Qin
author_facet	Qiuyan Huo Yu Yin Fangfang Liu Yuying Ma Liming Wang Guimin Qin
author_sort	Qiuyan Huo
title	Cell type identification from single-cell transcriptomes in melanoma
title_short	Cell type identification from single-cell transcriptomes in melanoma
title_full	Cell type identification from single-cell transcriptomes in melanoma
title_fullStr	Cell type identification from single-cell transcriptomes in melanoma
title_full_unstemmed	Cell type identification from single-cell transcriptomes in melanoma
title_sort	cell type identification from single-cell transcriptomes in melanoma
publisher	BMC
publishDate	2021
url	https://doaj.org/article/376d7da8df7b4c7ba77f56a0d0d526ba
work_keys_str_mv	AT qiuyanhuo celltypeidentificationfromsinglecelltranscriptomesinmelanoma AT yuyin celltypeidentificationfromsinglecelltranscriptomesinmelanoma AT fangfangliu celltypeidentificationfromsinglecelltranscriptomesinmelanoma AT yuyingma celltypeidentificationfromsinglecelltranscriptomesinmelanoma AT limingwang celltypeidentificationfromsinglecelltranscriptomesinmelanoma AT guiminqin celltypeidentificationfromsinglecelltranscriptomesinmelanoma
_version_	1718419237911920640

Cell type identification from single-cell transcriptomes in melanoma

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