MADS: A new and improved method for analysis of differential alternative splicing by exon-tiling microarrays
MADS: A new and improved method for analysis of differential alternative splicing by exon-tiling microarrays
复制标题
DOI：
10.1261/rna.1070208
复制
发表时间：
2008-08-01
期刊：
影响因子：
4.5
通讯作者：
Wong, Wing Hung
中科院分区：
文献类型：
--
作者：
Xing, Yi;Stoilov, Peter;Wong, Wing Hung
我们描述了一种方法，差异剪接的微阵列分析（MADS），发现差异选择性剪接的外显子平铺微阵列数据。MADS结合了一系列由外显子阵列的“富含探针”设计激发的低水平分析算法，包括背景校正、迭代探针选择和去除与脱靶转录物的序列特异性交叉杂交。我们使用MADS分析了小鼠神经母细胞瘤细胞系在shRNA介导的剪接因子多聚嘧啶束结合蛋白（PTB）敲低后的Affytek外显子1.0阵列数据。从具有响应于PTB耗竭的预定包含/排除概况的外显子列表中，MADS识别出已知在转录物包含水平中具有大的变化的所有外显子，并提供了对Affysses分析程序的改进。我们还鉴定了许多新的PTB依赖性剪接事件。30个新事件进行了RT-PCR检测，27个被证实。这项工作表明，外显子平铺微阵列设计是一个有效的和强大的方法，全球性的，公正的分析前mRNA剪接。
We describe a method, microarray analysis of differential splicing (MADS), for discovery of differential alternative splicing from exon-tiling microarray data. MADS incorporates a series of low-level analysis algorithms motivated by the "probe-rich'' design of exon arrays, including background correction, iterative probe selection, and removal of sequence-specific cross-hybridization to off-target transcripts. We used MADS to analyze Affymetrix Exon 1.0 array data on a mouse neuroblastoma cell line after shRNA-mediated knockdown of the splicing factor polypyrimidine tract binding protein (PTB). From a list of exons with predetermined inclusion/exclusion profiles in response to PTB depletion, MADS recognized all exons known to have large changes in transcript inclusion levels and offered improvement over Affymetrix's analysis procedure. We also identified numerous novel PTB-dependent splicing events. Thirty novel events were tested by RT-PCR and 27 were confirmed. This work demonstrates that the exon-tiling microarray design is an efficient and powerful approach for global, unbiased analysis of pre-mRNA splicing.