Open Access Method

Genomic analysis of early murine mammary gland development using novel probe-level algorithms

Stephen R Master1,2,4, Alexander J Stoddard1,4, L Charles Bailey1,4,5, Tien-Chi Pan1,4, Katherine D Dugan1,4 and Lewis A Chodosh1,3,4*

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Author affiliations

1 Department of Cancer Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160, USA

2 Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160, USA

3 Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160, USA

4 Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160, USA

5 Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA

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Citation and License

Genome Biology 2005, 6:R20 doi:10.1186/gb-2005-6-2-r20

Published: 1 February 2005

Abstract

We describe a novel algorithm (ChipStat) for detecting gene-expression changes utilizing probe-level comparisons of replicate Affymetrix oligonucleotide microarray data. A combined detection approach is shown to yield greater sensitivity than a number of widely used methodologies including SAM, dChip and logit-T. Using this approach, we identify alterations in functional pathways during murine neonatal-pubertal mammary development that include the coordinate upregulation of major urinary proteins and the downregulation of loci exhibiting reciprocal imprinting.