Table 4.

Breast cancer gene sets that are enriched in HFD microarray samples

GENE SET NAME	SIZE	ES	NES	NOM
				p-value
SMID_BREAST_CANCER_NORMAL_LIKE_UP	348	0.50	2.13	<0.001
POOLA_INVASIVE_BREAST_CANCER_UP	215	0.51	1.96	<0.001
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP	142	0.46	1.91	<0.001
FINAK_BREAST_CANCER_SDPP_SIGNATURE	21	0.65	1.87	<0.001
FINETTI_BREAST_CANCER_KINOME_GREEN	15	0.75	1.86	<0.001
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP	266	0.44	1.77	<0.001
SMID_BREAST_CANCER_LUMINAL_B_DN	412	0.36	1.69	<0.001
JOHNSTONE_PARVB_TARGETS_3_UP	306	0.34	1.64	<0.001

Gene set enrichment analysis was preformed with microarray data from high fat and low fat diet as described in the Materials and Methods and 361 curated breast cancer gene sets on the Molecular Signatures Database, Broad Institute. In GSEA enrichment scores (ES) are calculated for each gene set using a Kolmogorov-Smirnov-style statistic. The ES indicates how strongly associated a gene set is with a given phenotype or not. GSEA generates nominal p-values (NOM p-value) using on a phenotype based permutation comparing ES with a null distribution. Normalized enrichment scores (NES) are adjusted enrichment scores based on the number of genes in each examined set. Gene sets with a nominal P-value (NOM p-value) of 0.001 or less and a normalized enrichment score (NES) of 1.5 or greater are shown. These data suggest that common genes are expressed in mammary fat pads from mice treated with HFD and invasive breast cancer.