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.

To complete this recipe, we need a combined mouse gene expression data matrix and human breast cancer gene signatures.  Charles M Perou kindly provided the data matrices used in the original publication, in order to improve reproducibility by avoiding different data processing and normalization across various microarray datasets and platforms.  The data matrices were reformatted as gct and cls formats for Gene Set Enrichment Analysis.  The processed dataset (with annotation on the journal website) can be accessbile from GenomeSpace's Public folder.

In the original study, 17 distinct murine expression-based class (with Ex designation) were defined by SigClust analysis.  In this recipe, we will specifically examine the similarity between the human Basal-like subtype and murine C3TagEx class, mainly composed of two genetically engineered mouse models C3 Tag and Wap Tag.  Other subtypes can be investigated in a similar way and will not be covered in this recipe.

Provided file 1 (gene expression matrix): Perou_363Mouse_17SigClust.gct
​A combined gene expression matrix from 27 murine models.  22 outlying samples which didn't belong to any of the 17 expression-based class were excluded from the final expression data matrix.

Provided file 2 (phenotype labels): Perou_SigClust15_C3TagEx_vs_Others.cls

Class labels associated with each sample in the expression data.  For the pairwise Gene Set Enrichment Analysis in this recipe, label "0" denotes samples belonging to C3TagEx cluster and "1" denotes other samples.

Provided file 3 (Geneset database): c2.kegg.c7.all.v5.1_Perou_MouseGenesets_0513_2016.gmt

The customized geneset database is consisted of three sets.

a) CP:KEGG: KEGG gene sets (subset of C2: curated gene sets) from MSigDB.

b) C7: immunologic signatures (ImmuneSigDB, PMID: 26795250) from MSigDB.  These genesets are used to explore transcriptional programs in the human and mouse inmmune systems.

c) Customized genesets extracted by Supplemental Table 1 in the original manuscript.  These genesets (with prefix "Perou") are gene-expression signatures of human and mouse breast cancer subtypes.

We used ortholog gene assignments from Mouse Genome Informatics, retrieved from the MGI website on Jan 28, 2016.