IsoformSwitchAnalyzeR：全基因组范围内可变剪接模式变化及其功能后果的分析。

IsoformSwitchAnalyzeR: analysis of changes in genome-wide patterns of alternative splicing and its functional consequences.

机构信息

The Bioinformatics Centre, Department of Biology and Biotech Research & Innovation Centre, University of Copenhagen, 2200 Copenhagen N, Denmark.

出版信息

Bioinformatics. 2019 Nov 1;35(21):4469-4471. doi: 10.1093/bioinformatics/btz247.

DOI:10.1093/bioinformatics/btz247

PMID:30989184

Abstract

SUMMARY

Alternative splicing is an important mechanism involved in health and disease. Recent work highlights the importance of investigating genome-wide changes in splicing patterns and the subsequent functional consequences. Current computational methods only support such analysis on a gene-by-gene basis. Therefore, we extended IsoformSwitchAnalyzeR R library to enable analysis of genome-wide changes in specific types of alternative splicing and predicted functional consequences of the resulting isoform switches. As a case study, we analyzed RNA-seq data from The Cancer Genome Atlas and found systematic changes in alternative splicing and the consequences of the associated isoform switches.

AVAILABILITY AND IMPLEMENTATION

Windows, Linux and Mac OS: http://bioconductor.org/packages/IsoformSwitchAnalyzeR.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

可变剪接是涉及健康和疾病的重要机制。最近的研究强调了研究剪接模式的全基因组变化及其后续功能后果的重要性。目前的计算方法仅支持基于基因的此类分析。因此，我们扩展了 IsoformSwitchAnalyzeR R 库，以能够分析特定类型的可变剪接的全基因组变化，并预测由此产生的异构体转换的功能后果。作为案例研究，我们分析了来自癌症基因组图谱的 RNA-seq 数据，发现了可变剪接的系统变化以及相关异构体转换的后果。