Yaxin Chen1, Gang Wang1, Jingyi Li2, Lei Xia3, Lin Zhu1, Wenxing Li4, Qiang Luo2, Yinlu Liao2, Yao Lin2, Liyun Bi1, Hubin Chen2, Jiemei Chu2, Yueqi Li2, Jinming Su2, Li Ye2, Jun-Jun Jiang2, Hao Liang5, Weimin Li6, Sanqi An7. 1. Frontiers Science Center for Disease-Related Molecular Network, Precision Medicine Research Center, West China Hospital, Department of Respiratory and Critical Care Medicine, Sichuan University, Chengdu, Sichuan, China. 2. Biosafety Level-3 Laboratory, Life Sciences Institute & Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, 530021, Guangxi, China. 3. Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China. 4. Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China. 5. Biosafety Level-3 Laboratory, Life Sciences Institute & Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, 530021, Guangxi, China. lianghao@gxmu.edu.cn. 6. Frontiers Science Center for Disease-Related Molecular Network, Precision Medicine Research Center, West China Hospital, Department of Respiratory and Critical Care Medicine, Sichuan University, Chengdu, Sichuan, China. weimi003@scu.edu.cn. 7. Biosafety Level-3 Laboratory, Life Sciences Institute & Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, 530021, Guangxi, China. ansq@mail2.sysu.edu.cn.
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/ .
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/ .
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