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Learning from microarray interlaboratory studies: measures of precision for gene expression

Background The ability to demonstrate the reproducibility of gene expression microarray results is a critical consideration for the use of microarray technology in clinical applications. While studies have asserted that microarray data can be "highly reproducible" under given conditions, there is little ability to quantitatively compare amongst the various metrics and terminology ...

DNMT3b overexpression contributes to a hypermethylator phenotype in human breast cancer cell lines

Background DNA hypermethylation events and other epimutations occur in many neoplasms, producing gene expression changes that contribute to neoplastic transformation, tumorigenesis, and tumor behavior. Some human cancers exhibit a hypermethylator phenotype, characterized by concurrent DNA methylation-dependent silencing of multiple genes. To determine if a hypermethylation defect ...

Technical Reproducibility of Genotyping SNP Arrays Used in Genome-Wide Association Studies

During the last several years, high-density genotyping SNP arrays have facilitated genome-wide association studies (GWAS) that successfully identified common genetic variants associated with a variety of phenotypes. However, each of the identified genetic variants only explains a very small fraction of the underlying genetic contribution to the studied phenotypic trait. Moreover, ...

The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies

Leming Shi Wendell D Jones Roderick V Jensen Stephen C Harris Roger G Perkins Federico M Goodsaid Lei Guo Lisa J Croner Cecilie Boysen Hong Fang Feng Qian Shashi Amur Wenjun Bao Catalin C