Epigenetic signature of Gleason score and prostate cancer recurrence after radical prostatectomy

Clinical Epigenetics

Table 4 Gene Set Enrichment Analysis results

Gene set name	Description	NES
Positive enrichment score
HALLMARK_E2F_TARGETS	Genes encoding cell cycle-related targets of E2F transcription factors	3.86
HALLMARK_G2M_CHECKPOINT	Genes involved in the G2/M checkpoint, as in progression through the cell division cycle	3.08
HALLMARK_MITOTIC_SPINDLE	Genes important for mitotic spindle assembly	2.19
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION	Genes defining epithelial-mesenchymal transition, as in wound healing, fibrosis, and metastasis	2.15
HALLMARK_ALLOGRAFT_REJECTION	Genes upregulated during transplant rejection	1.96
HALLMARK_MYC_TARGETS_V1	A subgroup of genes regulated by MYC—version 1 (v1)	1.87
Negative enrichment score
HALLMARK_ANDROGEN_RESPONSE	Genes defining response to androgens	−2.83
HALLMARK_FATTY_ACID_METABOLISM	Genes encoding proteins involved in metabolism of fatty acids	−2.04
HALLMARK_XENOBIOTIC_METABOLISM	Genes encoding proteins involved in processing of drugs and other xenobiotics	−1.98

We identified genes that showed increased expression with higher levels of the epigenetic signature (FDR Q < 0.05; n = 1108) or decreased expression with higher levels of the signature (FDR Q < 0.05; n = 1357). These genes were pre-ranked according to Pearson correlation, and this pre-ranked list was used as input for GSEA. The gene sets in the table have an FDR Q value < 0.05. A positive value for the NES indicates that higher levels of the signature were associated with increased expression of the genes in a gene set
FDR false discovery rate, NES normalized enrichment score

ISSN: 1868-7083