Singular Value Decomposition-Based Alternative Splicing Detection

• 成果类型: Article
• 署名作者: Hu, Jianhua; He, Xuming; Cote, Gilbert J.; Krahe, Ralf
• 署名单位: University of Texas System; UTMD Anderson Cancer Center; University of Texas System; UTMD Anderson Cancer Center; University of Texas System; UTMD Anderson Cancer Center; University of Illinois System; University of Illinois Urbana-Champaign
• 刊物名称: JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
• ISSN/ISSBN: 0162-1459
• DOI: 10.1198/jasa.2009.ap08283
• 发表日期: 2009
• 页码: 944-953
• 关键词: gene-expression; variants; sequence; receptor; genome

摘要

Altered alternative splicing has been identified as an important factor in tumorigenesis. The Affymetrix exon tiling array is designed for detecting alternative splicing events in a transcriptome-wide fashion; however. there are currently few analysis tools that have been well Studied for effective detection of alternative splicing events. We propose a new screening procedure based on singular value decomposition (SVD) of the residual matrix from a robust additive model fit to probe selection region (PSR) data. With this approach, we analyze the exon filing array data from a brain cancer Study conducted at the M. D. Anderson Cancer Center, and show that the proposed SVD-based approach is able to better accommodate outlying measures and capitalize on the multidimensional group-by-PSR gene expression profiles for more effective detection of group-specific alternative splicing events. as well as the PSRs most likely associated with the alternative splicing. Lab validation confirmed some of our findings. but the list of candidates detected with Our proposed method may provide a better signpost to guide further investigations.