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Table 4 Gene Set Enrichment Analysis results

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

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
  1. 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
  2. FDR false discovery rate, NES normalized enrichment score