Database Commons

a catalog of worldwide biological databases

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.

Alternative splicing (AS) represents a crucial method in mRNA level to regulate gene expression and contributes to the protein complexity. Abnormal splicing has been reported to play roles in several diseases, including cancers. We developed the OncoSplicing database for visualization of survival-associated and differential alternative splicing in 2019. Here, we provide an updated version of OncoSplicing for an integrative view of clinically relevant alternative splicing based on 122 423 AS events across 33 cancers in the TCGA SpliceSeq project and 238 558 AS events across 32 cancers in the TCGA SplAdder project. The new version of the database contains several useful features, such as annotation of alternative splicing-associated transcripts, survival analysis based on median and optimal cut-offs, differential analysis between TCGA tumour samples and adjacent normal samples or GTEx normal samples, pan-cancer views of alternative splicing, splicing differences and results of Cox'PH regression, identification of clinical indicator-relevant and cancer-specific splicing events, and downloadable splicing data in the SplAdder project. Overall, the substantially updated version of OncoSplicing (www.oncosplicing.com) is a user-friendly and registration-free database for browsing and searching clinically relevant alternative splicing in human cancers.