CASA : a comprehensive database resource for the COVID-19 Alternative Splicing Atlas
© 2022. The Author(s)..
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/.
| Medienart: |
E-Artikel |
|---|
| Erscheinungsjahr: |
2022 |
|---|---|
| Erschienen: |
2022 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:20 |
|---|---|
| Enthalten in: |
Journal of translational medicine - 20(2022), 1 vom: 20. Okt., Seite 473 |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Chen, Yaxin [VerfasserIn] |
|---|
| Links: |
|---|
| Themen: |
63231-63-0 |
|---|
| Anmerkungen: |
Date Completed 24.10.2022 Date Revised 03.11.2023 published: Electronic Citation Status MEDLINE |
|---|
| doi: |
10.1186/s12967-022-03699-8 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
NLM347813704 |
|---|
| LEADER | 01000naa a22002652 4500 | ||
|---|---|---|---|
| 001 | NLM347813704 | ||
| 003 | DE-627 | ||
| 005 | 20231226034727.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 231226s2022 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1186/s12967-022-03699-8 |2 doi | |
| 028 | 5 | 2 | |a pubmed24n1159.xml |
| 035 | |a (DE-627)NLM347813704 | ||
| 035 | |a (NLM)36266726 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a Chen, Yaxin |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a CASA |b a comprehensive database resource for the COVID-19 Alternative Splicing Atlas |
| 264 | 1 | |c 2022 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ƒaComputermedien |b c |2 rdamedia | ||
| 338 | |a ƒa Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Date Completed 24.10.2022 | ||
| 500 | |a Date Revised 03.11.2023 | ||
| 500 | |a published: Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a © 2022. The Author(s). | ||
| 520 | |a 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 | ||
| 520 | |a 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 | ||
| 520 | |a 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/ | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, Non-U.S. Gov't | |
| 650 | 7 | |a RNA-Binding Proteins |2 NLM | |
| 650 | 7 | |a RNA |2 NLM | |
| 650 | 7 | |a 63231-63-0 |2 NLM | |
| 700 | 1 | |a Wang, Gang |e verfasserin |4 aut | |
| 700 | 1 | |a Li, Jingyi |e verfasserin |4 aut | |
| 700 | 1 | |a Xia, Lei |e verfasserin |4 aut | |
| 700 | 1 | |a Zhu, Lin |e verfasserin |4 aut | |
| 700 | 1 | |a Li, Wenxing |e verfasserin |4 aut | |
| 700 | 1 | |a Luo, Qiang |e verfasserin |4 aut | |
| 700 | 1 | |a Liao, Yinlu |e verfasserin |4 aut | |
| 700 | 1 | |a Lin, Yao |e verfasserin |4 aut | |
| 700 | 1 | |a Bi, Liyun |e verfasserin |4 aut | |
| 700 | 1 | |a Chen, Hubin |e verfasserin |4 aut | |
| 700 | 1 | |a Chu, Jiemei |e verfasserin |4 aut | |
| 700 | 1 | |a Li, Yueqi |e verfasserin |4 aut | |
| 700 | 1 | |a Su, Jinming |e verfasserin |4 aut | |
| 700 | 1 | |a Ye, Li |e verfasserin |4 aut | |
| 700 | 1 | |a Jiang, Jun-Jun |e verfasserin |4 aut | |
| 700 | 1 | |a Liang, Hao |e verfasserin |4 aut | |
| 700 | 1 | |a Li, Weimin |e verfasserin |4 aut | |
| 700 | 1 | |a An, Sanqi |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Journal of translational medicine |d 2003 |g 20(2022), 1 vom: 20. Okt., Seite 473 |w (DE-627)NLM142679194 |x 1479-5876 |7 nnns |
| 773 | 1 | 8 | |g volume:20 |g year:2022 |g number:1 |g day:20 |g month:10 |g pages:473 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1186/s12967-022-03699-8 |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a GBV_NLM | ||
| 951 | |a AR | ||
| 952 | |d 20 |j 2022 |e 1 |b 20 |c 10 |h 473 | ||