Open Access Method

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

Stephen R Master124, Alexander J Stoddard14, L Charles Bailey145, Tien-Chi Pan14, Katherine D Dugan14 and Lewis A Chodosh134*

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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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.