Experimental comparison and evaluation of the Affymetrix exon and U133Plus2 GeneChip arrays.
Experimental comparison and evaluation of the Affymetrix exon and U133Plus2 GeneChip arrays.
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Affymetrix外显子和U133PLUS2 Genechip阵列的实验比较和评估。
DOI：
10.1371/journal.pone.0000913
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发表时间：
2007-09-19
期刊：
影响因子：
3.7
通讯作者：
Triche, Timothy J.
中科院分区：
文献类型：
--
作者：
Abdueva, Diana;Wing, Michele R.;Schaub, Betty;Triche, Timothy J.
Affytron外显子阵列为科学家提供了在单个阵列上进行全基因组规模的外显子水平表达谱分析的唯一解决方案。这些阵列的特点是一个新的芯片设计，没有错配探针和一个全新的随机引物协议，以产生正义DNA目标沿着整个长度的转录本。除了这些变化之外，有限数量的验证实验和几乎没有实验数据来严格解决全外显子阵列与传统3′阵列的可比性，导致自然不愿意用新的全外显子平台取代传统表达阵列。使用市售的Affytron阵列，我们直接通过一系列在固定真核背景存在下含有25个转录物的“加标”杂交来评估人外显子1.0 ST（HuEx）和U133 Plus 2.0（U133Plus2）平台的性能。具体而言，我们比较了HuEx和U133Plus2阵列的表达测量，以评估这些测量的精度以及测量检测差异表达能力的特异性和灵敏度。本研究提出了一个实验比较和系统的交叉验证的Affyellow外显子阵列，并建立了高可比性的表达变化和探针的性能特征之间的Affyellow常规和外显子阵列。此外，这项研究提供了一个可靠的基准数据集的竞争外显子表达措施的比较，选择适合映射外显子阵列措施的方法，以丰富的先前生成的微阵列数据，以及开发更先进的方法外显子和转录水平的表达总结。
Affymetrix exon arrays offer scientists the only solution for exon-level expression profiling at the whole-genome scale on a single array. These arrays feature a new chip design with no mismatch probes and a radically new random primed protocol to generate sense DNA targets along the entire length of the transcript. In addition to these changes, a limited number of validating experiments and virtually no experimental data to rigorously address the comparability of all-exon arrays with conventional 3′-arrays result in a natural reluctance to replace conventional expression arrays with the new all-exon platform. Using commercially available Affymetrix arrays, we assess the performance of the Human Exon 1.0 ST (HuEx) and U133 Plus 2.0 (U133Plus2) platforms directly through a series of ‘spike-in’ hybridizations containing 25 transcripts in the presence of a fixed eukaryotic background. Specifically, we compare the measures of expression for HuEx and U133Plus2 arrays to evaluate the precision of these measures as well as the specificity and sensitivity of the measures' ability to detect differential expression. This study presents an experimental comparison and systematic cross-validation of Affymetrix exon arrays and establishes high comparability of expression changes and probe performance characteristics between Affymetrix conventional and exon arrays. In addition, this study offers a reliable benchmark data set for the comparison of competing exon expression measures, the selection of methods suitable for mapping exon array measures to the wealth of previously generated microarray data, as well as the development of more advanced methods for exon- and transcript-level expression summarization.
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影响因子：
14.9
作者：
Abdueva D;Skvortsov D;Tavaré S
通讯作者：
Tavaré S
影响因子：
14.9
作者：
Zhang, Li;Wu, Chunlei;Zhao, Haitao
通讯作者：
Zhao, Haitao
DOI：
10.2165/00822942-200605030-00003
发表时间：
2006-01-01
期刊：
Applied bioinformatics
影响因子：
--
作者：
Zhang, Yongqing;Ferreira, Antonio;Zhang, Jiong
通讯作者：
Zhang, Jiong
影响因子：
3.4
作者：
Halperin, A;Buhot, A;Zhulina, EB
通讯作者：
Zhulina, EB
影响因子：
14.9
作者：
Hekstra, D;Taussig, AR;Naef, F
通讯作者：
Naef, F