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Table 2 Histone marks and biological terms enriched by the genes in each module

From: Gene co-expression and histone modification signatures are associated with melanoma progression, epithelial-to-mesenchymal transition, and metastasis

Module Histone marks Biological terms Database
Turquoise H3K27me3 Axon guidance GO biological process
Regulation of MAP kinase activity
Extracellular matrix organization Reactome
Delta-Notch signaling pathway KEGG
Glycosaminoglycan biosynthesis
Focal Adhesion-PI3K-Akt-mTOR-signaling pathway WikiPathways
Alpha6-Beta4 Integrin signaling pathway
TGF Beta signaling pathway
Blue H3K79me3, H3K79me2, H3K27ac, H3K4me3, H3K36me3, H4K20me1 Cellular response to DNA damage stimulus GO biological process
Mitochondrial translation
Ubiquitination and proteasome degradation Reactome
Negative regulation of MAPK pathway
Proteasome degradation WikiPathways
TNF-alpha NF-kB signaling pathway
Protein processing in endoplasmic reticulum KEGG
Yellow H3K4me3, H3K36me3 Mitochondrion organization GO biological process
Hippo signaling pathway KEGG
Red - Regulation of cell migration GO biological process
Cell cycle Reactome
Axon guidance KEGG
Hippo signaling pathway KEGG
DNA replication KEGG
G1 to S cell cycle control WikiPathways
ESC pluripotency pathways WikiPathways
Black H3K27ac, H3K79me2 Activation of JUN kinase activity GO biological process
Positive regulation of apoptotic process
Regulation of small GTPase signal transduction
TNF signaling pathway KEGG
Regulation of actin cytoskeleton KEGG
Protein processing in endoplasmic reticulum KEGG
Tight junction KEGG
Regulation of actin cytoskeleton WikiPathways
Wnt signaling pathway and pluripotency WikiPathways
Magenta H3K27ac, H3K4me3 mRNA splicing GO biological process
Double-strand break repair
DNA replication WikiPathways
Nucleotide excision repair KEGG
Spliceosome KEGG
Purple H3K79me2, H3K36me3 Protein ubiquitination GO biological process
RNA processing
Insulin signaling pathway KEGG
Endocytosis KEGG
Ribosome KEGG
Delta-Notch signaling pathway WikiPathways
Wnt signaling pathway WikiPathways
Greenyellow H3K79me2 Triglyceride biosynthesis Reactome
Autophagosome organization GO biological process
Positive regulation of cytoskeleton organization
Ras protein signal transduction
Tan - Base excision repair KEGG
Signaling by Rho GTPases Reactome
DNA repair Reactome
Regulation of cell cycle GO biological process
Protein ubiquitination
Salmon - Regulation of toll-like receptor signaling pathway WikiPathways
Focal adhesion KEGG
ECM-receptor interaction KEGG
p75 NTR receptor-mediated signaling Reactome
Cell cycle KEGG
Midnight blue - Focal adhesion KEGG
Insulin receptor signaling cascade Reactome
Signaling events mediated by VEGFR NCI-NATURE
Positive regulation of MAP kinase activity GO biological process
Neutrophile degranulation
Light cyan H3K79me2 HATs acetylate histones Reactome
Regulation of mitotic cell cycle GO biological process
Pink H3K27ac Regulation of mRNA stability GO biological process
Proteasomal protein catabolic process GO biological process
Brown H3K79me2, H3K27ac, HeK4me3, H3ac, H3K9ac, H3K36me3 mRNA processing WikiPathways
Homologous recombination KEGG
Cell cycle Reactome
Cellular response to DNA damage stimulus GO biological process
  1. The functions, pathways, and histone marks were considered to be significantly enriched if their adjusted p values were less than 0.05