Can subtle changes in gene expression be consistently detected with different microarray platforms?
Can subtle changes in gene expression be consistently detected with different microarray platforms?
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DOI：
10.1186/1471-2164-9-124
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发表时间：
2008-03-10
期刊：
影响因子：
4.4
通讯作者：
de Menezes RX
中科院分区：
文献类型：
--
作者：
Pedotti P;'t Hoen PA;Vreugdenhil E;Schenk GJ;Vossen RH;Ariyurek Y;de Hollander M;Kuiper R;van Ommen GJ;den Dunnen JT;Boer JM;de Menezes RX
不同微阵列平台产生的基因表达数据的可比性仍然是一个值得关注的问题。在这里，我们讨论了在具有挑战性的生物学背景下，在基因表达差异很少且微妙的情况下，五种不同的微阵列平台检测差异表达基因的性能和重叠。采用Applied Biosystems、Affymetrix、Agilent、Illumina、LGTC home-spotted arrays等5个芯片平台，对5只野生型和5只转基因δ c -双皮质素样激酶小鼠海马中的基因表达谱进行了评估。使用10%的固定错误发现率，我们检测到每个平台差异表达基因数量之间的惊人差异。ABI筛选了4个基因，Affymetrix筛选了130个，Agilent筛选了3051个，Illumina筛选了54个，LGTC筛选了13个。2个基因在所有平台上均有显著差异表达，ABI平台鉴定的4个基因在至少3个其他平台上均有发现。定量RT-PCR分析证实了两个或多个平台检测到的28个基因中的20个，仅Agilent检测到的15个基因中的8个。我们观察到，与固定的统计截止值相比，基于显著性水平对基因进行排序时，平台之间的相关性有所改善。我们证明了不同平台识别的受影响基因集的显著重叠，尽管生物过程仅由部分重叠的基因集表示。所有平台均一致发现转基因小鼠中gaba能信号的异常。不同的微阵列平台对受影响的生物过程给出了部分互补的观点。我们的数据表明，在分析基因表达只有细微差异的样本时，使用两种不同的平台可能比增加重复次数更有吸引力。商业双色平台似乎在寻找表达差异较小的群体之间的差异表达基因方面具有更高的能力。
The comparability of gene expression data generated with different microarray platforms is still a matter of concern. Here we address the performance and the overlap in the detection of differentially expressed genes for five different microarray platforms in a challenging biological context where differences in gene expression are few and subtle. Gene expression profiles in the hippocampus of five wild-type and five transgenic δC-doublecortin-like kinase mice were evaluated with five microarray platforms: Applied Biosystems, Affymetrix, Agilent, Illumina, LGTC home-spotted arrays. Using a fixed false discovery rate of 10% we detected surprising differences between the number of differentially expressed genes per platform. Four genes were selected by ABI, 130 by Affymetrix, 3,051 by Agilent, 54 by Illumina, and 13 by LGTC. Two genes were found significantly differentially expressed by all platforms and the four genes identified by the ABI platform were found by at least three other platforms. Quantitative RT-PCR analysis confirmed 20 out of 28 of the genes detected by two or more platforms and 8 out of 15 of the genes detected by Agilent only. We observed improved correlations between platforms when ranking the genes based on the significance level than with a fixed statistical cut-off. We demonstrate significant overlap in the affected gene sets identified by the different platforms, although biological processes were represented by only partially overlapping sets of genes. Aberrances in GABA-ergic signalling in the transgenic mice were consistently found by all platforms. The different microarray platforms give partially complementary views on biological processes affected. Our data indicate that when analyzing samples with only subtle differences in gene expression the use of two different platforms might be more attractive than increasing the number of replicates. Commercial two-color platforms seem to have higher power for finding differentially expressed genes between groups with small differences in expression.
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影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
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：
14.9
作者：
Barnes M;Freudenberg J;Thompson S;Aronow B;Pavlidis P
通讯作者：
Pavlidis P
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
DOI：
10.1073/pnas.0601231103
发表时间：
2006-04-11
影响因子：
11.1
作者：
Ein-Dor, L;Zuk, O;Domany, E
通讯作者：
Domany, E