Generation and validation of mouse mammary squamous tumor signature.

<p>(A)Tumor histologies observed in a study MMTV-PyMT tumors[<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007135#pgen.1007135.ref054" target="_blank">54</a>].(B) Venn diagram illustrating the number of genes identified in each comparison using significance analysis of microarrays, 184 genes were commonly identified and proposed as signature genes. (C) Heatmap representation of unsupervised hierarchical clustering of MMTV-PyMT tumors limited to squamous signature genes shows performance of the signature on the training dataset. Levels of RMA normalized median centered expression values are shown according the colorbar. Genes expression data is deposited on GEO datasets GSE104397. (D) Heatmap representation of unsupervised hierarchical clustering of MMTV-Myc tumors limited to squamous signature genes shows performance of the signature on the validation dataset. Levels of RMA normalized median centered expression values are shown according the colorbar. (E) Gene set enrichment analysis testing for enrichment of the proposed squamous signature genes shows significant enrichment in MMTV-Myc squamous tumors (normalized enrichment score, NES = 1.48, nominal p-value = 0.0, FDR q-value = 0.029).