HiChIP is an effective high-resolution contact map generation method with low read depth (Mumbach et al., Nat. Methods, 2016) . Recent years have witnessed a surge in HiChIP assays across various cell types, which have helped to characterize functional relevance of looping interactions and provide extraordinary insights into diseases arising from mutations in different sources, such as epigenetic modifiers, transcription factors (TFs), TF-binding loci, and architectural proteins (Weintraub et al., Cell, 2017; Simeonov et al., Nature, 2017). To facilitate studies of 3D regulatory interactions and their potential roles in transcriptional control during normal development and disease, we curated this comprehensive HiChIP database, HiChIPdb. We aim to offer a promising avenue for researchers to investigate genome-wide chromatin interactions across different cell types in the context of various proteins of interest.

To date, HiChIPdb contains:
    1. 200 high-throughput HiChIP experiments with 12 kinds of ChIPs across 108 different cell types.
HiChIPdb has the following main features:
human body
Eye human_Eye
Breast human_Breast
Stomach human_Stomach
Intestine human_Intestine
Kidney human_Kidney
Muscle human_Muscle
Skin human_Skin
Brain human_Brain
Lung human_Lung
Heart human_Heart
Stem cell Stem cell
Blood human_Blood
Ovary human_Ovary
Esophagus human_Esophagus
Uterus human_Uterus
Embryo human_Embryo
Prostate human_Prostate
Thyroid human_Thyroid
Lymph human_Lymph

Recent articles

Gibbin mesodermal regulation patterns epithelial development. Collier A, Liu A, Torkelson J, et al.Nature. 2022;606(7912):188-96.
Understanding 3D genome organization by multidisciplinary methods. Jerkovic I, Cavalli G. Nature Reviews Molecular Cell Biology. 2021;22(8):511-28.
UTX condensation underlies its tumour-suppressive activity. Shi B, Li W, Song Y, et al. Nature. 2021;597(7878):726-31.
Super enhancers define regulatory subtypes and cell identity in neuroblastoma. Gartlgruber M, Sharma AK, Quintero A, et al. Nature Cancer. 2021;2(1):114-28.
HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Mumbach M R, Rubin A J, Flynn R A, et al. Nature Methods. 2016, 13(11): 919-922.

News and updates

  • Add the gene and GWAS catalog annotation at different scales.

    19 June 2022
  • Provided a demo of HiChIP dataset analysis.

    15 May 2022
  • Version 1.0 of the database is launched.

    03 March 2022