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Table 2 Pathways enriched for BRAF mutation-associated promoter methylation after exclusion of ES cell H3K27me 3 binding promoter regions

From: BRAF mutation-specific promoter methylation of FOX genes in colorectal cancer

BRAF mutation-specific promoters (125) Associated genes Expected hitsa Hits P b
Hedgehog signaling pathway SMO; GSK3Ac; CREBBPc 0.16 3 0.000561
PI3 kinase pathway FOXB1; FOXB2; FOXD3; CCND1; GSK3Ac 0.72 5 0.000849
Insulin/IGF pathway-protein kinase B signaling cascade FOXB1; FOXB2; FOXD3; GSK3Ac 0.56 4 0.00252
Wnt signaling pathway NKD2c; GNG4; CCND1; GSK3Ac; CREBBPc; AXIN1; LEF1 1.99 7 0.00405
Transcription regulation by bZIP transcription factor MTERF; CREBBPcTAF7 0.33 3 0.00471
  1. aExpected hits: expected number of hits by chance in the reference gene list; bP values of the binomial test between the BRAF mutation-specific gene list and the reference gene list; c targets with low tumor/normal log2 ratios in the BRAF wildtype group, suggesting that additional mechanisms, such as genomic loss, may play a role.