Fig. 3

a) Enrichment plots showing the correlation of gene sets from breast cancer amplicons 16p13 (FDR q-value 0.106) and 22q13 (FDR q-value 0.101) with the PRA phenotype. Profile of the running enrichment score and positions of gene set members on the rank-ordered list (upregulation or downregulation of genes in PRA transgenics relative to their expression in wild-type). b) Enrichment map visualization of gene-sets correlating with down regulated genes in PRA transgenics showing manually identified clusters defined as (i) gene sets related to mammary gland morphological changes or breast cancer subtypes; (ii) gene sets related to estradiol or tamoxifen response and (iii) gene sets comprising targets of polycomb complexes. In the similarity network node size represents the number of genes in the gene-set; edge thickness is proportional to the overlap between gene-sets and the enrichment score is mapped to the node color as a color gradient, in this case blue (high enrichment in wild-type)