Alternative splicing (AS) is a crucial mechanism to regulate gene expression and protein complexity. RNA-binding proteins (RBPs) play an important role in regulating abnormal alternative splicing in cancers. However, few resources are available to identify specific RBPs responsible for regulating individual AS event. We have developed the OncoSplicing database for integrative analysis of clinically relevant alternative splicing events in TCGA cancers. Here, we further updated the OncoSplicing database by performing correlation analysis between the splicing and mRNA expression data from the TCGA cancers or GTEx tissues, mapping known RNA-binding motifs and eCLIP-seq peaks to all AS events, conducting splicing analysis for RNA-seq data from RBP perturbation experiments in the ENCODE project, and integrating exon and intron sequences for each AS event. With this updated database, users can easily identify potential RBPs responsible for the queried AS event and obtain sequences to design AS-specific primers and minigene constructs for experiment validation. Overall, compared to the previous version, the substantially updated OncoSplicing database (www.oncosplicing.com) offers a more valuable resource for users to identify RBPs responsible for regulating alternative splicing events in cancers.
基金:
National Natural Science Foundation of China [82070726, 82270803, 82203365]; China Postdoctoral Science Foundation [2022M722464]; Jiangxi Provincial Natural Science Foundation [20232BAB206090]
第一作者机构:[1]Wuhan Univ, Zhongnan Hosp, Canc Precis Diag & Treatment & Translat Med Hubei, Wuhan 430000, Peoples R China[2]Wuhan Univ, Zhongnan Hosp, Dept Biol Repositories, Wuhan 430000, Peoples R China[3]Wuhan Univ, Zhongnan Hosp, Dept Urol, Wuhan 430000, Peoples R China[4]Univ Sci & Technol China, Affiliated Hosp USTC 1, Dept Urol, Div Life Sci & Med, Hefei 230000, Peoples R China
共同第一作者:
通讯作者:
通讯机构:[1]Wuhan Univ, Zhongnan Hosp, Canc Precis Diag & Treatment & Translat Med Hubei, Wuhan 430000, Peoples R China[2]Wuhan Univ, Zhongnan Hosp, Dept Biol Repositories, Wuhan 430000, Peoples R China[3]Wuhan Univ, Zhongnan Hosp, Dept Urol, Wuhan 430000, Peoples R China[8]Wuhan Univ, TaiKang Ctr Life & Med Sci, Wuhan 430000, Peoples R China
推荐引用方式(GB/T 7714):
Zhang Yangjun,Liu Kai,Xu Zhenzhen,et al.OncoSplicing 3.0: an updated database for identifying RBPs regulating alternative splicing events in cancers[J].NUCLEIC ACIDS RESEARCH.2024,doi:10.1093/nar/gkae1098.
APA:
Zhang, Yangjun,Liu, Kai,Xu, Zhenzhen,Li, Bo,Wu, Xiaoliang...&Xu, Hua.(2024).OncoSplicing 3.0: an updated database for identifying RBPs regulating alternative splicing events in cancers.NUCLEIC ACIDS RESEARCH,,
MLA:
Zhang, Yangjun,et al."OncoSplicing 3.0: an updated database for identifying RBPs regulating alternative splicing events in cancers".NUCLEIC ACIDS RESEARCH .(2024)