Epigenomic Features

TF binding site

TF binding sites from ChIP-seq experiments.

Possible relationships:

TF_binding_site -[overlap/locate_in/downstream/upstream]- (any entities with coordinates)

Histone binding site

Histone binding sites from ChIP-seq experiments.

Possible relationships:

Histone_binding_site -[overlap/locate_in/downstream/upstream]- (any entities with coordinates)

DNase hypersensitivity site(DHS)

Open chromosome regions from ChIP-seq experiments.

Possible relationships:

DNase_hypersensitivity_site -[overlap/locate_in/downstream/upstream]- (any entities with coordinates)

TF binding motif

DNA motifs that a specific TF binds to.

Possible relationships:

TF_binding_motif -[overlap/locate_in/downstream/upstream]- (any entities with coordinates)

Replication timing

Replication timing refers to the order in which segments of DNA along the length of a chromosome are duplicated. We include early/late two-stage timing in GenomicKB.

Possible relationships:

replication_timing -[overlap/locate_in/downstream/upstream]- (any entities with coordinates)

ChromHMM state

ChromHMM is software for learning and characterizing chromatin states. The 15-state results are included in GenomicKB.

Possible relationships:

ChromHMM_state -[overlap/locate_in/downstream/upstream]- (any entities with coordinates)