Analysis of high fat diet induced genes during mammary gland development: identifying role players in poor prognosis of breast cancer

Table 5 HFD leads to a loss in the expression of luminal genes

GENE SET NAME	Size	ES	NES	NOM
GENE SET NAME	Size	ES	NES	p-value
SMID_BREAST_CANCER_NORMAL_LIKE_UP	348	0.50	2.09	<0.001
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP	142	0.47	1.95	<0.001
FINETTI_BREAST_CANCER_KINOME_GREEN	15	0.75	1.84	0.01
SMID_BREAST_CANCER_LUMINAL_B_DN	412	0.37	1.70	<0.001
FARMER_BREAST_CANCER_CLUSTER_1	25	0.66	1.70	0.01
CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_DN	325	0.33	1.53	0.01
HOWLIN_PUBERTAL_MAMMARY_GLAND	60	0.40	1.50	0.03

Gene set enrichment analysis was performed with 53 gene sets containing luminal genes in breast cancer denoted (form 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. We found that gene sets with down-regulation of luminal genes were enriched in the HFD samples.

ISSN: 1756-0500