NDLI: CASA: a comprehensive database resource for the COVID-19 Alternative Splicing Atlas

Content Provider	Springer Nature : BioMed Central
Author	Chen, Yaxin Wang, Gang Li, Jingyi Xia, Lei Zhu, Lin Li, Wenxing Luo, Qiang Liao, Yinlu Lin, Yao Bi, Liyun Chen, Hubin Chu, Jiemei Li, Yueqi Su, Jinming Ye, Li Jiang, Jun-jun Liang, Hao Li, Weimin An, Sanqi
Abstract	Background As a key process in transcriptional regulatory mechanisms, alternative splicing (AS) plays a crucial role in maintaining the diversity of RNA and protein expression, and mediates the immune response in infectious diseases, especially for the COVID-19. Therefore, urgent data gathering and more research of AS profiles in microbe-infected human cells are needed to improve understanding of COVID-19 and related infectious diseases. Herein, we have created CASA, the COVID-19 Alternative Splicing Atlas to provide a convenient computing platform for studies of AS in COVID-19 and COVID-19-related infectious diseases. Methods In CASA, we reanalyzed thousands of RNA-seq datasets generated from 65 different tissues, organoids and cell lines to systematically obtain quantitative data on AS events under different conditions. A total of 262,994 AS events from various infectious diseases with differing severity were detected and visualized in this database. In order to explore the potential function of dynamics AS events, we performed analysis of functional annotations and drug-target interactions affected by AS in each dataset. RNA-binding proteins (RBPs), which may regulate these dynamic AS events are also provided for users in this database. Results CASA displays microbe-induced alterations of the host cell splicing landscape across different virus families and helps users identify condition-specific splicing patterns, as well as their potential regulators. CASA may greatly facilitate the exploration of AS profiles and novel mechanisms of host cell splicing by viral manipulation. CASA is freely available at http://www.splicedb.net/casa/ .
Related Links	https://translational-medicine.biomedcentral.com/counter/pdf/10.1186/s12967-022-03699-8.pdf
Ending Page	10
Page Count	10
Starting Page	1
File Format	HTM / HTML
ISSN	14795876
DOI	10.1186/s12967-022-03699-8
Journal	Journal of Translational Medicine
Issue Number	1
Volume Number	20
Language	English
Publisher	BioMed Central
Publisher Date	2022-10-20
Access Restriction	Open
Subject Keyword	Biomedicine Medicine Public Health Medicine/Public Health
Content Type	Text
Resource Type	Article
Subject	Biochemistry, Genetics and Molecular Biology Medicine
Journal Impact Factor	6.1/2023
5-Year Journal Impact Factor	6.3/2023

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