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^,4^,3

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

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

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

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

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

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Genome Biology 2005, 6:R20doi:10.1186/gb-2005-6-2-r20


Published:	1 February 2005

Subject areas: Genome studies, Bioinformatics, Development, Methods

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.