Detect the Different Isoforms Using GeneChip Human Exon 1.0 ST Arrays

2009 2nd International Conference on Biomedical Engineering and Informatics Pub Date : 2009-10-30 DOI:10.1109/BMEI.2009.5305187

Mi-Chia Ma, Hsiao-Fang Lin, Ying Xu

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Abstract

Alternative splicing is the RNA splicing variation mechanism. The exon isoforms lead to numerous different expressions through the alternative splicing. It’s imperative to find the carcinogenic gene from the massive quantity of genes and understand the expressed isoforms. In this paper, the statistical procedures are applied on the colon cancer sample data of Affymetrix GeneChip Human Exon 1.0 ST Array and the dataset is used as the example of finding isoforms. First, the Wilcoxon sign rank test was applied to choose the suspect carcinogenic genes. About 54,854 suspect genes are selected from original 312,368 genes at 5% significant level. Second, one sample t-test and the factor analysis are used to estimate the tumor and normal isoforms for each suspect carcinogenic gene, respectively. Furthermore, the confirmations are made by comparing the estimated results with Alternative Splicing Database. Finally, the results may be provided to the biologist to make biological confirmations and discover the new isoforms. Keywords-alternative splicing; exon array; colon cancer; isoform

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使用GeneChip Human Exon 1.0 ST阵列检测不同的异构体

选择性剪接是RNA剪接变异机制。外显子异构体通过选择性剪接导致许多不同的表达。从大量的基因中找到致癌基因并了解其表达的同工型是当务之急。本文将统计程序应用于Affymetrix GeneChip Human Exon 1.0 ST Array的结肠癌样本数据，并以该数据集为例进行同种异构体的发现。首先，采用Wilcoxon符号秩检验选择可疑致癌基因。从原始的312368个基因中，以5%的显著性水平筛选出54854个可疑基因。其次，使用单样本t检验和因子分析分别估计每个可疑致癌基因的肿瘤和正常亚型。并将估计结果与Alternative Splicing Database进行了比较。最后，这些结果可以提供给生物学家进行生物学确认和发现新的异构体。Keywords-alternative拼接;外显子数组;结肠癌;同种型

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2009 2nd International Conference on Biomedical Engineering and Informatics

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