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