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Table 1 Risk-active pathways identified by the proposed method (iDRW+DA)

From: Integrative pathway-based survival prediction utilizing the interaction between gene expression and DNA methylation in breast cancer

Pathway ID Pathway name Frequencya Total genesb DE genes DM genes
map 04320 Dorso-ventral axis formation 10/50 27 4 0
map 04972 Pancreatic secretion 8/50 65 26 3
map 04722 Neurotrophin signaling pathway 7/50 90 47 3
map 05020 Prion diseases 7/50 30 12 0
map 00670 One carbon pool by folate 5/50 33 6 1
map 00592 alpha-Linolenic acid metabolism 5/50 23 8 1
map 00620 Pyruvate metabolism 5/50 96 7 1
map 03320 PPAR signaling pathway 5/50 61 13 1
map 04660 T cell receptor signaling pathway 5/50 85 52 8
map 04510 Focal adhesion 5/50 148 83 11
map 03010 Ribosome 5/50 143 1 0
map 05214 Glioma 5/50 52 27 0
map 04711 Circadian rhythm - fly 5/50 8 4 1
map 00960 Tropane, piperidine, and pyridine alkaloid biosynthesis 5/50 26 1 0
  1. aFrequency: the number of times the pathway has been selected over 10 times of 5-fold cross validation process (50 iterations)
  2. bTotal genes: the number of genes mapped to the pathway in the KEGG database
  3. Note that the number of differentially expressed genes (DE genes) and differentially methylated genes (DM genes) are also shown (p-value of DESeq2 or t-test < 0.05)