CardioAtlas: deciphering the single-cell transcriptome landscape in cardiovascular tissues and diseases
Abstract Increasing scRNA-seq data in cardiovascular research have substantially improved our knowledge on the development of the cardiovascular system and the mechanisms underlying cardiovascular diseases. However, the single-cell transcriptome datasets were dispersed in literature and no resource...
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| Format: | Article |
| Language: | English |
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BMC
2024-11-01
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| Series: | Biomarker Research |
| Online Access: | https://doi.org/10.1186/s40364-024-00696-5 |
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| _version_ | 1846147564673433600 |
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| author | Tiantongfei Jiang Xiaoyan Jin Yueying Gao Weiwei Zhou Jinyang Yu Yongsheng Li Juan Xu Benzhi Cai |
| author_facet | Tiantongfei Jiang Xiaoyan Jin Yueying Gao Weiwei Zhou Jinyang Yu Yongsheng Li Juan Xu Benzhi Cai |
| author_sort | Tiantongfei Jiang |
| collection | DOAJ |
| description | Abstract Increasing scRNA-seq data in cardiovascular research have substantially improved our knowledge on the development of the cardiovascular system and the mechanisms underlying cardiovascular diseases. However, the single-cell transcriptome datasets were dispersed in literature and no resource for cardiovascular systems and diseases. Here, we constructed an organized resource CardioAtlas, which provides comprehensive analysis results for > 1,929,000 cells in 27 human data sets and > 1,088,000 cells in 39 mouse data sets. Through large-scale literature retrieval and manual annotation, we constructed 12 and 15 scRNA-seq reference atlas for common human and mouse cardiovascular systems and diseases, covering 43 and 39 cell types. In particular, CardioAtlas provides five analytic modules, including cell-type prediction, identification of marker genes, functional enrichment analysis, identification of cell-type-specific transcription regulons, and cell-cell communication analysis. In addition, users can upload scRNA-seq data for personalized analysis. CardioAtlas is available at http://bio-bigdata.hrbmu.edu.cn/CardioAtlas . CardioAtlas provides the first comprehensive and well-crafted reference atlas of cardiovascular systems and diseases and describes in detail previously unrecognized cell populations across a large number of humans and mice. |
| format | Article |
| id | doaj-art-27c658b0538a4ec59f3b60a54549f5f6 |
| institution | Kabale University |
| issn | 2050-7771 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Biomarker Research |
| spelling | doaj-art-27c658b0538a4ec59f3b60a54549f5f62024-12-01T12:38:10ZengBMCBiomarker Research2050-77712024-11-011211510.1186/s40364-024-00696-5CardioAtlas: deciphering the single-cell transcriptome landscape in cardiovascular tissues and diseasesTiantongfei Jiang0Xiaoyan Jin1Yueying Gao2Weiwei Zhou3Jinyang Yu4Yongsheng Li5Juan Xu6Benzhi Cai7College of Bioinformatics Science and Technology, Harbin Medical UniversityDepartment of Pharmacy, The Second Affiliated Hospital, Department of Pharmacology, College of Pharmacy, (The Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), Harbin Medical UniversitySchool of Interdisciplinary Medicine and Engineering, Harbin Medical UniversityCollege of Bioinformatics Science and Technology, Harbin Medical UniversityHainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Department of Reproductive Medicine, Hainan Provincial Clinical Research Center for Thalassemia, Key Laboratory of Reproductive Health Diseases Research and Translation, College of Biomedical Information and Engineering, Hainan Medical University, Ministry of Education, The First Affiliated Hospital of Hainan Medical UniversitySchool of Interdisciplinary Medicine and Engineering, Harbin Medical UniversityCollege of Bioinformatics Science and Technology, Harbin Medical UniversityDepartment of Pharmacy, The Second Affiliated Hospital, Department of Pharmacology, College of Pharmacy, (The Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), Harbin Medical UniversityAbstract Increasing scRNA-seq data in cardiovascular research have substantially improved our knowledge on the development of the cardiovascular system and the mechanisms underlying cardiovascular diseases. However, the single-cell transcriptome datasets were dispersed in literature and no resource for cardiovascular systems and diseases. Here, we constructed an organized resource CardioAtlas, which provides comprehensive analysis results for > 1,929,000 cells in 27 human data sets and > 1,088,000 cells in 39 mouse data sets. Through large-scale literature retrieval and manual annotation, we constructed 12 and 15 scRNA-seq reference atlas for common human and mouse cardiovascular systems and diseases, covering 43 and 39 cell types. In particular, CardioAtlas provides five analytic modules, including cell-type prediction, identification of marker genes, functional enrichment analysis, identification of cell-type-specific transcription regulons, and cell-cell communication analysis. In addition, users can upload scRNA-seq data for personalized analysis. CardioAtlas is available at http://bio-bigdata.hrbmu.edu.cn/CardioAtlas . CardioAtlas provides the first comprehensive and well-crafted reference atlas of cardiovascular systems and diseases and describes in detail previously unrecognized cell populations across a large number of humans and mice.https://doi.org/10.1186/s40364-024-00696-5 |
| spellingShingle | Tiantongfei Jiang Xiaoyan Jin Yueying Gao Weiwei Zhou Jinyang Yu Yongsheng Li Juan Xu Benzhi Cai CardioAtlas: deciphering the single-cell transcriptome landscape in cardiovascular tissues and diseases Biomarker Research |
| title | CardioAtlas: deciphering the single-cell transcriptome landscape in cardiovascular tissues and diseases |
| title_full | CardioAtlas: deciphering the single-cell transcriptome landscape in cardiovascular tissues and diseases |
| title_fullStr | CardioAtlas: deciphering the single-cell transcriptome landscape in cardiovascular tissues and diseases |
| title_full_unstemmed | CardioAtlas: deciphering the single-cell transcriptome landscape in cardiovascular tissues and diseases |
| title_short | CardioAtlas: deciphering the single-cell transcriptome landscape in cardiovascular tissues and diseases |
| title_sort | cardioatlas deciphering the single cell transcriptome landscape in cardiovascular tissues and diseases |
| url | https://doi.org/10.1186/s40364-024-00696-5 |
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