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.

中文翻译：

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OncoSplicing 3.0：用于识别调节癌症选择性剪接事件的 RBP 的更新数据库


选择性剪接 （AS） 是调节基因表达和蛋白质复杂性的重要机制。RNA 结合蛋白 （RBP） 在调节癌症中的异常选择性剪接中起重要作用。然而，很少有资源可用于识别负责调节单个 AS 事件的特定 RBP。我们开发了 OncoSplicing 数据库，用于对 TCGA 癌症中临床相关的选择性剪接事件进行综合分析。在这里，我们通过对来自 TCGA 癌症或 GTEx 组织的剪接和 mRNA 表达数据进行相关性分析，将已知的 RNA 结合基序和 eCLIP-seq 峰映射到所有 AS 事件，对来自 ENCODE 项目中 RBP 扰动实验的 RNA-seq 数据进行剪接分析，并整合每个 AS 事件的外显子和内含子序列。借助这个更新的数据库，用户可以轻松识别导致查询的 AS 事件的潜在 RBP，并获得序列以设计 AS 特异性引物和小基因构建体以进行实验验证。总体而言，与以前的版本相比，大幅更新的 OncoSplicing 数据库 （www.oncosplicing.com） 为用户提供了更有价值的资源，以识别负责调节癌症中可变剪接事件的 RBP。