Comparative gene expression analysis in mouse models for identifying critical pathways in mammary gland development

Functional development of the mammary gland is an important physiological process. Several studies have used gene expression profiling of mammary gland development to identify the key genes in the process, but few focused on the involved pathways. And there is a lack of concordance between those observed pathways. In this article, we applied a standardized microarray preprocessing to four independent studies, and then used gene set enrichment analysis (GSEA) to identify the key pathways. The result demonstrated an increased concordance between these expression profiling data sets. From the stage of puberty to pregnancy, we found 7 up-regulated and 6 down-regulated pathways in common. From the period of pregnancy to lactation, we found 7 up-regulated and 58 down-regulated pathways in common. And 10 up-regulated and 3 down-regulated pathways were found in common from lactation to the involution period. The main canonical pathways identified belong to immune system, cell communication, metabolism, and disease-related pathways. Pathway analysis is a more effective method than single gene analysis because the former one can able to detect genes weakly connected to the phenotype. As we applied GSEA to the study, our findings suggested a greater concordance in this physiological process. The critical pathways we find can provide some insight of functional development of the mammary gland and motivate other relative studies.