MSdb: An integrated expression atlas of human musculoskeletal system
Summary: The global prevalence and burden of musculoskeletal (MSK) disorders are immense. Advancements in next-generation sequencing (NGS) have generated vast amounts of data, accelerating the research of pathological mechanisms and the development of therapeutic approaches for MSK disorders. Howeve...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-06-01
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| Series: | iScience |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004223010106 |
| _version_ | 1797814328403951616 |
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| author | Ruonan Tian Ziwei Xue Dengfeng Ruan Pengwei Chen Yiwen Xu Chao Dai Weiliang Shen Hongwei Ouyang Wanlu Liu Junxin Lin |
| author_facet | Ruonan Tian Ziwei Xue Dengfeng Ruan Pengwei Chen Yiwen Xu Chao Dai Weiliang Shen Hongwei Ouyang Wanlu Liu Junxin Lin |
| author_sort | Ruonan Tian |
| collection | DOAJ |
| description | Summary: The global prevalence and burden of musculoskeletal (MSK) disorders are immense. Advancements in next-generation sequencing (NGS) have generated vast amounts of data, accelerating the research of pathological mechanisms and the development of therapeutic approaches for MSK disorders. However, scattered datasets across various repositories complicate uniform analysis and comparison. Here, we introduce MSdb, a database for visualization and integrated analysis of next-generation sequencing data from human musculoskeletal system, along with manually curated patient phenotype data. MSdb provides various types of analysis, including sample-level browsing of metadata information, gene/miRNA expression, and single-cell RNA-seq dataset. In addition, MSdb also allows integrated analysis for cross-samples and cross-omics analysis, including customized differentially expressed gene/microRNA analysis, microRNA-gene network, scRNA-seq cross-sample/disease integration, and gene regulatory network analysis. Overall, systematic categorizing, standardized processing, and freely accessible knowledge features MSdb a valuable resource for MSK research community. |
| first_indexed | 2024-03-13T08:06:02Z |
| format | Article |
| id | doaj.art-32065d08472b49b1a8dfdcc12b24125c |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-03-13T08:06:02Z |
| publishDate | 2023-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-32065d08472b49b1a8dfdcc12b24125c2023-06-01T04:36:50ZengElsevieriScience2589-00422023-06-01266106933MSdb: An integrated expression atlas of human musculoskeletal systemRuonan Tian0Ziwei Xue1Dengfeng Ruan2Pengwei Chen3Yiwen Xu4Chao Dai5Weiliang Shen6Hongwei Ouyang7Wanlu Liu8Junxin Lin9Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, Zhejiang 314100, ChinaZhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, Zhejiang 314100, ChinaZhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, ChinaZhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, ChinaZhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, ChinaZhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, ChinaDr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Department of Sports Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Hangzhou, Zhejiang 310058, China; China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, Zhejiang 310058, ChinaZhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Department of Sports Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Hangzhou, Zhejiang 310058, China; China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, Zhejiang 310058, China; Corresponding authorZhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, Zhejiang 314100, China; Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Hangzhou, Zhejiang 310058, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Zhejiang University, Hangzhou, Zhejiang 310058, China; Corresponding authorZhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Corresponding authorSummary: The global prevalence and burden of musculoskeletal (MSK) disorders are immense. Advancements in next-generation sequencing (NGS) have generated vast amounts of data, accelerating the research of pathological mechanisms and the development of therapeutic approaches for MSK disorders. However, scattered datasets across various repositories complicate uniform analysis and comparison. Here, we introduce MSdb, a database for visualization and integrated analysis of next-generation sequencing data from human musculoskeletal system, along with manually curated patient phenotype data. MSdb provides various types of analysis, including sample-level browsing of metadata information, gene/miRNA expression, and single-cell RNA-seq dataset. In addition, MSdb also allows integrated analysis for cross-samples and cross-omics analysis, including customized differentially expressed gene/microRNA analysis, microRNA-gene network, scRNA-seq cross-sample/disease integration, and gene regulatory network analysis. Overall, systematic categorizing, standardized processing, and freely accessible knowledge features MSdb a valuable resource for MSK research community.http://www.sciencedirect.com/science/article/pii/S2589004223010106BioinformaticsBiological databaseGenomicsTranscriptomics |
| spellingShingle | Ruonan Tian Ziwei Xue Dengfeng Ruan Pengwei Chen Yiwen Xu Chao Dai Weiliang Shen Hongwei Ouyang Wanlu Liu Junxin Lin MSdb: An integrated expression atlas of human musculoskeletal system iScience Bioinformatics Biological database Genomics Transcriptomics |
| title | MSdb: An integrated expression atlas of human musculoskeletal system |
| title_full | MSdb: An integrated expression atlas of human musculoskeletal system |
| title_fullStr | MSdb: An integrated expression atlas of human musculoskeletal system |
| title_full_unstemmed | MSdb: An integrated expression atlas of human musculoskeletal system |
| title_short | MSdb: An integrated expression atlas of human musculoskeletal system |
| title_sort | msdb an integrated expression atlas of human musculoskeletal system |
| topic | Bioinformatics Biological database Genomics Transcriptomics |
| url | http://www.sciencedirect.com/science/article/pii/S2589004223010106 |
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