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

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/.

SpliceWiz: interactive analysis and visualization of alternative splicing in R

“…AS databases, whereby AS quantitation has been performed on large RNA-seq datasets in advance, are in growing demand. Recently, numerous AS databases have been published, covering various biological systems including diverse human and murine tissues [ 34 , 35 ], cancers [ 36–38 ] and COVID-19 [ 39 ]. SpliceWiz provides an ideal platform to create AS databases due to its ability to uniformly analyse and package data from large datasets.…”

Scm6A: A fast and low-cost method for quantifying m6A modifications at the single-cell level

“…The dysregulation of immune responses in COVID-19 patients has emerged as a primary factor affecting symptoms and mortality rates [31,32]. Consequently, the investigation of relevant immune cells has become a focal point in combatting this disease [33,34].…”