Skip to main content

Table 4 Top enriched gene ontology annotations on CpG probes with beta regression coefficient values < − 200 in association with ionizing radiations using conditional logistic regression EWAS on the methionine dependency phenotype

From: Ionizing radiations induce shared epigenomic signatures unraveling adaptive mechanisms of cancerous cell lines with or without methionine dependency

GO biological process complete CLR-EWAS for the methionine dependency phenotype (MeWo-LC1 vs. MeWo)
FE* P-value FDR, P-value
Positive regulation of protein targeting to mitochondrion (GO:1903955) 3.00 1.03 × 10–3 4.57 × 10–2
Regulation of protein targeting to mitochondrion (GO:1903214) 2.80 3.50 × 10–4 1.87 × 10–2
Mitotic metaphase plate congression (GO:0007080) 2.60 5.84 × 10–4 2.87 × 10–2
Embryonic digit morphogenesis (GO:0042733) 2.51 4.70 × 10–4 2.40 × 10–2
Metaphase plate congression (GO:0051310) 2.47 5.38 × 10–4 2.67 × 10–2
Positive regulation of establishment of protein localization to mitochondrion (GO:1903749) 2.40 9.12 × 10–4 4.19 × 10–2
Mitotic G1 DNA damage checkpoint signaling (GO:0031571) 2.35 4.65 × 10–4 2.38 × 10–2
Regulation of establishment of protein localization to mitochondrion (GO:1903747) 2.30 3.61 × 10–4 1.91 × 10–2
Intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630) 2.30 6.77 × 10–4 3.24 × 10–2
Mitotic G1/S transition checkpoint signaling (GO:0044819) 2.30 5.24 × 10–4 2.62 × 10–2
Protein N-linked glycosylation (GO:0006487) 2.30 6.84 × 10–4 3.25 × 10–2
Mitotic sister chromatid segregation (GO:0000070) 2.20 4.52 × 10–5 3.31 × 10–3
Intrinsic apoptotic signaling pathway (GO:0097193) 2.11 1.65 × 10–5 1.43 × 10–3
Negative regulation of G1/S transition of mitotic cell cycle (GO:2000134) 2.05 3.93 × 10–4 2.05 × 10–2
G1/S transition of mitotic cell cycle (GO:0000082) 2.05 6.21 × 10–4 3.00 × 10–2
Mitotic cell cycle checkpoint signaling (GO:0007093) 2.03 2.85 × 10–5 2.26 × 10–3
Mitotic DNA damage checkpoint signaling (GO:0044773) 2.02 3.85 × 10–4 2.02 × 10–2
Cell cycle G1/S phase transition (GO:0044843) 2.01 9.98 × 10–4 4.47 × 10–2
Mitotic DNA integrity checkpoint signaling (GO:0044774) 2.01 3.16 × 10–4 1.73 × 10–2
  1. CLR: conditional logistic regression; FE: fold enrichment; DFR: false discovery rate
  2. *Top significantly enriched GO annotations were defined using a Q–Q plot ranking of fold enrichment values. The full list of significantly enriched gene ontology annotations is reported in Additional file 13: Table S7b