Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms.
Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms.
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DOI：
10.1093/nar/gkn705
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发表时间：
2008-12
影响因子：
14.9
通讯作者：
den Dunnen JT
中科院分区：
文献类型：
--
作者：
't Hoen PA;Ariyurek Y;Thygesen HH;Vreugdenhil E;Vossen RH;de Menezes RX;Boer JM;van Ommen GJ;den Dunnen JT
采用Solexa/Illumina深度测序技术和5种不同的微阵列平台比较野生型小鼠和δ C-双皮质素样激酶转基因小鼠的海马表达谱。通过Illumina的数字基因表达检测，我们每个样本获得了1240万个序列标签，它们的丰度跨越了四个数量级。结果是高度可重复的，即使在实验室之间。使用专用的贝叶斯模型，我们发现了3179个转录本的差异表达，估计错误发现率为8.5%。这一数字比微阵列高得多。使用深度测序和微阵列发现的差异表达转录物的重叠对于Affyellow最显著。通过深度测序观察到的表达变化大于通过微阵列或定量PCR观察到的变化。相关的过程，如钙调蛋白依赖性蛋白激酶活性和囊泡运输沿着微管被发现受到影响的深度测序，但不受微阵列。虽然微阵列检测不到，反义转录发现的所有基因的51%和替代多聚腺苷酸化的47%。我们的结论是，深度测序在表达谱数据的稳健性、可比性和丰富性方面取得了重大进展，预计将促进协作、比较和整合基因组学研究。
The hippocampal expression profiles of wild-type mice and mice transgenic for δC-doublecortin-like kinase were compared with Solexa/Illumina deep sequencing technology and five different microarray platforms. With Illumina's digital gene expression assay, we obtained ∼2.4 million sequence tags per sample, their abundance spanning four orders of magnitude. Results were highly reproducible, even across laboratories. With a dedicated Bayesian model, we found differential expression of 3179 transcripts with an estimated false-discovery rate of 8.5%. This is a much higher figure than found for microarrays. The overlap in differentially expressed transcripts found with deep sequencing and microarrays was most significant for Affymetrix. The changes in expression observed by deep sequencing were larger than observed by microarrays or quantitative PCR. Relevant processes such as calmodulin-dependent protein kinase activity and vesicle transport along microtubules were found affected by deep sequencing but not by microarrays. While undetectable by microarrays, antisense transcription was found for 51% of all genes and alternative polyadenylation for 47%. We conclude that deep sequencing provides a major advance in robustness, comparability and richness of expression profiling data and is expected to boost collaborative, comparative and integrative genomics studies.
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影响因子：
3.4
作者：
Evans, SJ;Datson, NA;Akil, H
通讯作者：
Akil, H
影响因子：
48
作者：
Cloonan, Nicole;Forrest, Alistair R. R.;Grimmond, Sean M.
通讯作者：
Grimmond, Sean M.
影响因子：
46.9
作者：
Canales, Roger D.;Luo, Yuling;Goodsaid, Federico M.
通讯作者：
Goodsaid, Federico M.
影响因子：
2.6
作者：
Feldker, DEM;de Kloet, ER;Datson, NA
通讯作者：
Datson, NA
DOI：
10.1186/bcr1604
发表时间：
2006
期刊：
Breast cancer research : BCR
影响因子：
--
作者：
Grigoriadis A;Mackay A;Reis-Filho JS;Steele D;Iseli C;Stevenson BJ;Jongeneel CV;Valgeirsson H;Fenwick K;Iravani M;Leao M;Simpson AJ;Strausberg RL;Jat PS;Ashworth A;Neville AM;O'Hare MJ
通讯作者：
O'Hare MJ