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Normalization and analysis of cDNA microarrays using within-array replications applied to neuroblastoma cell response to a cytokine
- Source :
- Proceedings of the National Academy of Sciences. 101:1135-1140
- Publication Year :
- 2004
- Publisher :
- Proceedings of the National Academy of Sciences, 2004.
-
Abstract
- The quantitative comparison of two or more microarrays can reveal, for example, the distinct patterns of gene expression that define different cellular phenotypes or the genes that are induced in the cellular response to certain stimulations. Normalization of the measured intensities is a prerequisite of such comparisons. However, a fundamental problem in cDNA microarray analysis is the lack of a common standard to compare the expression levels of different samples. Several normalization protocols have been proposed to overcome the variabilities inherent in this technology. We have developed a normalization procedure based on within-array replications via a semilinear in-slide model, which adjusts objectively experimental variations without making critical biological assumptions. The significant analysis of gene expressions is based on a weighted t statistic, which accounts for the heteroscedasticity of the observed log ratios of expressions, and a balanced sign permutation test. We illustrated the use of the techniques in a comparison of the expression profiles of neuroblastoma cells that were stimulated with a growth factor, macrophage migration inhibitory factor (MIF). The analysis of expression changes at mRNA levels showed that approximately 99 genes were up-regulated and 24 were reduced significantly (P<br />published_or_final_version
- Subjects :
- Normalization (statistics)
Multidisciplinary
Microarray analysis techniques
Gene Expression Profiling
Neuroblastoma - genetics - pathology
Computational biology
Biology
Molecular biology
Phenotype
Gene expression profiling
Neuroblastoma
Macrophage Migration-Inhibitory Factors - pharmacology
Tumor progression
Complementary DNA
Physical Sciences
Gene expression
Humans
DNA microarray
Macrophage Migration-Inhibitory Factors
Oligonucleotide Array Sequence Analysis
Subjects
Details
- ISSN :
- 10916490 and 00278424
- Volume :
- 101
- Database :
- OpenAIRE
- Journal :
- Proceedings of the National Academy of Sciences
- Accession number :
- edsair.doi.dedup.....e87016be61a155f99a8ee9ea410cae2c