title: Genomic analysis of early murine mammary gland development using novel probe-level algorithms.
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.
authors.affiliation: Department of Cancer Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160, USA. srmaster@mail.med.upenn.edu
authors.forename: Stephen R
authors.initials: SR
authors.lastname: Master
authors.forename: Alexander J
authors.initials: AJ
authors.lastname: Stoddard
authors.forename: L Charles
authors.initials: LC
authors.lastname: Bailey
authors.forename: Tien-Chi
authors.initials: TC
authors.lastname: Pan
authors.forename: Katherine D
authors.initials: KD
authors.lastname: Dugan
authors.forename: Lewis A
authors.initials: LA
authors.lastname: Chodosh
mesh_terms: D000465:Algorithms; D000818:Animals; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D023281:Genomics / Q000379:methods; D008321:Mammary Glands, Animal / Q000254:growth & development* / Q000378:metabolism*; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes
chemical_list: D015345:Oligonucleotide Probes