Sources of variability and effect of experimental approach on expression profiling data interpretation.
Sources of variability and effect of experimental approach on expression profiling data interpretation.
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DOI：
10.1186/1471-2105-3-4
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发表时间：
2002
影响因子：
3
通讯作者：
Hoffman EP
中科院分区：
文献类型：
--
作者：
Bakay M;Chen YW;Borup R;Zhao P;Nagaraju K;Hoffman EP
我们使用从人类肌肉活检中分离的 56 个 RNA（34 个 Affymetrix MuscleChip 阵列）和 36 个鼠细胞培养物和组织 RNA（42 个 Affymetrix U74Av2 阵列）对表达谱数据变异性的来源进行了系统研究。我们研究了 28 名人类受试者的肌肉活检以及小鼠生肌细胞培养物、肌肉和脾脏。使用人类 MuscleChip 阵列（4,601 个探针组）和鼠 U74Av2 Affymetrix 微阵列进行表达谱分析。 RNA 既可以单独进行分析，也可以作为混合组进行分析。研究的变量包括组织异质性、cRNA 探针产生、患者诊断和基因芯片杂交。我们发现，变异性的最大来源通常是同一患者肌肉活检的不同区域，反映了细胞类型含量的变化，即使在肌肉等相对同质的组织中也是如此。患者之间的差异也非常高（SNP 噪声）。实验变异（RNA、cDNA、cRNA 或 GeneChip）很小。患者 cRNA 样本的预分析混合有效地标准化了患者内部和患者间的变异来源，同时保留了个体分析的高度特异性（通过绝对分析检测到 86% 的统计显着性差异；通过 4 配对比较生存法检测到 85%）。使用 76 个寡核苷酸微阵列上的 92 个 RNA 样本的无监督聚类分析和相关系数，我们发现实验误差并不是表达谱实验中不必要的变异的重要来源。变异性的主要来源是小组织活检的使用，特别是在人类中，患者之间存在很大的变异性（SNP 噪声）。
We provide a systematic study of the sources of variability in expression profiling data using 56 RNAs isolated from human muscle biopsies (34 Affymetrix MuscleChip arrays), and 36 murine cell culture and tissue RNAs (42 Affymetrix U74Av2 arrays). We studied muscle biopsies from 28 human subjects as well as murine myogenic cell cultures, muscle, and spleens. Human MuscleChip arrays (4,601 probe sets) and murine U74Av2 Affymetrix microarrays were used for expression profiling. RNAs were profiled both singly, and as mixed groups. Variables studied included tissue heterogeneity, cRNA probe production, patient diagnosis, and GeneChip hybridizations. We found that the greatest source of variability was often different regions of the same patient muscle biopsy, reflecting variation in cell type content even in a relatively homogeneous tissue such as muscle. Inter-patient variation was also very high (SNP noise). Experimental variation (RNA, cDNA, cRNA, or GeneChip) was minor. Pre-profile mixing of patient cRNA samples effectively normalized both intra- and inter-patient sources of variation, while retaining a high degree of specificity of the individual profiles (86% of statistically significant differences detected by absolute analysis; and 85% by a 4-pairwise comparison survival method). Using unsupervised cluster analysis and correlation coefficients of 92 RNA samples on 76 oligonucleotide microarrays, we found that experimental error was not a significant source of unwanted variability in expression profiling experiments. Major sources of variability were from use of small tissue biopsies, particularly in humans where there is substantial inter-patient variability (SNP noise).
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影响因子：
14.9
作者：
Mills, JC;Gordon, JI
通讯作者：
Gordon, JI
影响因子：
56.9
作者：
Golub, TR;Slonim, DK;Lander, ES
通讯作者：
Lander, ES
DOI：
10.1073/pnas.96.16.9212
发表时间：
1999-08-03
影响因子：
11.1
作者：
Perou, CM;Jeffrey, SS;Botstein, D
通讯作者：
Botstein, D
影响因子：
3.3
作者：
Spellman, PT;Sherlock, G;Futcher, B
通讯作者：
Futcher, B
影响因子：
56.9
作者：
Winzeler, EA;Richards, DR;Davis, RW
通讯作者：
Davis, RW