Welcome to OncoSplicing!


OncoSplicing is a database to systematically study clinically relevant alternative splicing in 33 TCGA cancers and 31 GTEx tissues. Alternative splicing (AS) represents a crucial method in mRNA level to regulate gene expression, and contributes to the mRNA processing and protein complexity. Many researches have indicated that alternative splicing could be potential biomarkers for cancer diagnosis and drug targets for treatment. We developed the first version of OncoSplicing in 2019 to view survival associated and differential AS events in cancers, based on a majority of splicing data from the TCGA SpliceSeq database. Recently, we added splicing data of 31 GTEx tissues as well as 32 TCGA cancers from the SplAdder project, which contained much more novel AS events. In summary, a total of 122,423 AS events in the SpliceSeq project and 238,558 AS events in the SplAdder project were included in this database.


In the latest version of OncoSplicing, we integrated 282,125 splice events from two sources: 57,172 SpliceSeq events involving a single alternative exon, and 238,558 SplAdder events. We then mapped these events with RNA-binding motifs for 130 RBPs, eCLIP peaks for 150 RBPs, and splice events regulated by 358 RBPs from the ENCODE project. Correlation analyses were conducted for all integrated events with 753 unique RBPs, including both the collected RBPs and an additional 521 splicing regulators annotated in MsigDB. As a result, we identified 58,993,935 (27.8% of all) AS event-RBP pairs with at least one regulatory relationship, and 1,412,583 (0.7% of all) were classified as high-confidence.


In OncoSplicing, users can:


1. Browse or search a gene symbol for integrative AS information of the queried gene, including chromosomal location, AS associated transcripts and statistic results;

2. Browse or search a gene symbol in a cancer type to identify survival associated and/or differential AS events and to perform visualization;

3. Browse or search a gene symbol and select a splice event for pan-cancer views of PSI distribution in TCGA cancers and/or GTEx tissues and results of survival and/or differential analyses;

4. Browse or search a gene symbol in a cancer type to identify clinical indicator relevant AS events;

5. Download all results of analysis, figures of querying and PSI data in the SplAdder project for further integrative study.


In the latest OncoSplicing, users can also:


6. Search by gene symbol, AS event, or RBP to explore integrative splicing relationships between AS events and hundreds of RBPs.

7. Search by gene symbol, AS event, or RBP to investigate regulatory relationships between AS events and hundreds of RBPs from the ENCODE project.

8. Conduct co-expression analysis between different omics data, including splicing data and mRNA expression of RBPs, across TCGA and/or GTEx cohorts.



Updates in 2023!


1. 130 RBPs with 1,498 motifs were used to mapping to splice regions of all integrated 282,125 splice events.

2. 150 RBPs of 223 experiments in the ENCODE project with eCLIP peaks were used to mapping to all integrated splice events.

3. 358 RBPs of 716 experiments in the ENCODE project with raw RNA-seq data were re-analyzed to identify splicing regulation profiles.

4. 753 unique RBPs including all collected RBPs and other 521 MSigDB annotated splicing regulators were used to perform correlation analysis with PSI value of the integrated AS events in the TCGA or GTEx cohort.

5. Added the MapAS module to integrate the potential relationship between splice events and RBPs.

6. Added the Encode module for identifying and visualizing splicing events regulated by RBPs in the ENCODE project.

7. Added the CoExp module for co-expression analysis of different omics in TCGA or GTEx data sets.

Updates in 2021. gateio

1. Added AS events that with PSI values in less than 75% of samples in the TCGA SpliceSeq database.

2. Added 238,558 AS events across 32 TCGA cancers and 31 GTEx tissues from the SplAdder project.

3. Added the pan-cancer views of PSI values, results of survival and differential analyses for each AS event.

4. Added annotation of AS associated transcripts from genome annotation file (GRCh37/GENECODEv19) for most AS events.

5. Added the identification of AS events relevant to common clinical indicators.

6. Added the identification of 2590 cancer specific AS events in the SplAdder project.

Initial release in 2019. The 1st version

OncoSplicing was initially released in 2019 for visualization of survival associated alternative splicing for cancers in the TCGA SpliceSeq project.

Cite this website


Zhang Yangjun, Liu Kai, Xu zhenzhen, Li Bo, Wu Xiaoliang, Fan Ruixin, Yao Xiangyang, Wu Huahui, Duan Chen, Gong Yan, Chen Ke, Zeng Jin, Li Lu, Xu Hua. OncoSplicing 3.0: an updated database for identifying RBPs regulating alternative splicing events in cancers.

Zhang Yangjun, Yao Xiangyang, Zhou Hui, Wu Xiaoliang, Tian Jianbo, Zeng Jin, Yan Libin, Duan Chen, Liu Haoran, Li Heng, Chen Ke, Hu Zhiquan, Ye Zhangqun, Xu Hua. OncoSplicing: an updated database for clinically relevant alternative splicing in 33 human cancers. Nucleic Acids Res. 2021 Sep 23:gkab851. doi: 10.1093/nar/gkab851. PMID: 34554251.

Related publications


Zhang Yangjun, Wu Xiaoling, Li Jingzhen, Sun Kui, Li Heng, Yan Libin, Duan Chen, Liu Haoran, Chen Ke, Ye Zhangqun, Liu Mugen, Xu Hua. Comprehensive characterization of alternative splicing in renal cell carcinoma. Brief Bioinform. 2021 Sep 2;22(5):bbab084. doi: 10.1093/bib/bbab084. PMID: 33822848.

Zhang Yangjun, Yan Libin, Zeng Jin, Zhou Hui, Liu Haoran, Yu Gan, Yao Weimin, Chen Ke, Ye Zhangqun, Xu Hua. Pan-cancer analysis of clinical relevance of alternative splicing events in 31 human cancers. Oncogene.2019 Oct;38(40):6678-6695. doi:10.1038/s41388-019-0910-7. PMID: 31391553.