Cross-hybridization modeling on Affymetrix exon arrays.
Cross-hybridization modeling on Affymetrix exon arrays.
复制标题
Affymetrix外显子阵列上的跨杂交建模。
DOI：
10.1093/bioinformatics/btn571
复制
发表时间：
2008-12-15
期刊：
影响因子：
--
通讯作者：
Wong WH
中科院分区：
文献类型：
--
作者：
Kapur K;Jiang H;Xing Y;Wong WH
动机：微阵列设计已变得越来越探针丰富，使特定功能的目标，如个别外显子或单核苷酸多态性。这些阵列有可能实现转录丰度的定量高通量估计，但目前这些估计受到交叉杂交（探针与脱靶转录物杂交）引起的偏倚的影响。结果如下：为了研究交叉杂交，我们将Affytek外显子阵列探针映射到一组注释的mRNA转录本，允许两个序列之间的少量错配或插入/缺失。基于一个系统的研究，在何种程度上与一个给定的匹配类型的探针的成绩单受交叉杂交，我们开发了一种策略，以纠正交叉杂交的基因水平的表达估计偏差。与Solexa超高通量测序数据的比较表明，交叉杂交的校正导致基因表达估计值的显著改善。供货情况：我们提供人类和小鼠外显子阵列探针和脱靶转录本之间的映射，并提供扩展GeneBASE程序的软件，用于生成基因水平的表达估计，包括交叉杂交校正http://biogibbs.stanford.edu/~kkapur/GeneBase/。联系方式：whwong@stanford.edu补充信息：补充数据可从生物信息学在线网站获得。
Motivation: Microarray designs have become increasingly probe-rich, enabling targeting of specific features, such as individual exons or single nucleotide polymorphisms. These arrays have the potential to achieve quantitative high-throughput estimates of transcript abundances, but currently these estimates are affected by biases due to cross-hybridization, in which probes hybridize to off-target transcripts. Results: To study cross-hybridization, we map Affymetrix exon array probes to a set of annotated mRNA transcripts, allowing a small number of mismatches or insertion/deletions between the two sequences. Based on a systematic study of the degree to which probes with a given match type to a transcript are affected by cross-hybridization, we developed a strategy to correct for cross-hybridization biases of gene-level expression estimates. Comparison with Solexa ultra high-throughput sequencing data demonstrates that correction for cross-hybridization leads to a significant improve-ment of gene expression estimates. Availability: We provide mappings between human and mouse exon array probes and off-target transcripts and provide software extending the GeneBASE program for generating gene-level expression estimates including the cross-hybridization correction http://biogibbs.stanford.edu/~kkapur/GeneBase/. Contact: whwong@stanford.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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影响因子：
4.5
作者：
Xing, Yi;Stoilov, Peter;Wong, Wing Hung
通讯作者：
Wong, Wing Hung
影响因子：
3.7
作者：
Xing, Yi;Kapur, Karen;Wong, Wing Hung
通讯作者：
Wong, Wing Hung
DOI：
10.1073/pnas.011404098
发表时间：
2001-01-02
影响因子：
11.1
作者：
Li, C;Wong, WH
通讯作者：
Wong, WH
影响因子：
3
作者：
Smith AD;Xuan Z;Zhang MQ
通讯作者：
Zhang MQ
影响因子：
4.8
作者：
Srinivasan, K;Shiue, L;Ares, M
通讯作者：
Ares, M