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This recipe recapitulates research by Pfefferle et al., in Genome Biology(2013), "Transcriptomic classification of genetically engineered mouse models of breast cancer identifies human subtype counterparts", conducted by Charles M Perou's group.  This study encompasses the largest comprehensive genomic dataset to date to identify human-to-mouse disease subtype counterparts, consisting of three independent human breast cancer datasets and 385 DNA gene expression microarrays from 27 GEMMs of mammary carcinoma(Gene Expression Omnibus accession numbers GSE3165, GSE8516, GSE9343, GSE14457, GSE15263, GSE17916, GSE27101, and GSE42640).  In the original study, the similarity between specific human and mouse subtypes was measured using gene set analysis (GSA)(Table 2 in the publication).  To recapitulate this research, we will use Gene Set Enrichment Analysis module(v17) in GenePattern, as an independent method to further validate the research findings.  This effort is supported by NCI Oncology Models Forum(OMF), a collaborative effort to credential cancer mouse models for translational research.

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