ArticleNucleic acids research2023
HiChIPdb: a comprehensive database of HiChIP regulatory interactions.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- A multi-modal diffusion model with dual-cross-attention for multi-omics data generation and translation.Nature communications · 2026Article
- Silencer variants are key drivers of gene up-regulation in Alzheimer's disease.Science advances · 2026Article
- ChromPolymerDB: a high-resolution database of single-cell 3D chromatin structures for functional genomics.Nucleic acids research · 2026Article
- Massively parallel analysis of genotype-dependent enhancer activity among atopic dermatitis genetic risk variants.The Journal of allergy and clinical immunology · 2025Article
- Article
- ChromPolymerDB: A High-Resolution Database of Single-Cell 3D Chromatin Structures for Functional Genomics.bioRxiv : the preprint server for biology · 2025Article
- Deciphering functional landscape and clinical implications of enhancer RNAs in lung adenocarcinoma.Scientific reports · 2025Article
- CanASM: a comprehensive database for genome-wide allele-specific DNA methylation identification and annotation in cancer.BMC genomics · 2025Article
- Loop Catalog: a comprehensive HiChIP database of human and mouse samples.Genome biology · 2025Article
- Enhancer RNA-mediated transcriptional regulatory programs reveal the malignant progression of glioma.Science advances · 2025Article
- CREATE: cell-type-specific cis-regulatory element identification via discrete embedding.Nature communications · 2025Article
- Three-dimensional genome landscape of primary human cancers.Nature genetics · 2025Article
- Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants.Science (New York, N.Y.) · 2025Article
- Discovering the interactome, functions, and clinical relevance of enhancer RNAs in kidney renal clear cell carcinoma.BMC medical genomics · 2025Article
- EpiGePT: a pretrained transformer-based language model for context-specific human epigenomics.Genome biology · 2024Article
- A compendium of genetic variations associated with promoter usage across 49 human tissues.Nature communications · 2024Article
- Systematic identification of genotype-dependent enhancer variants in eosinophilic esophagitis.American journal of human genetics · 2024Article
- Genome-wide meta-analysis and fine-mapping prioritize potential causal variants and genes related to leprosy.MedComm · 2023Article
- DeepDrug: A general graph-based deep learning framework for drug-drug interactions and drug-target interactions prediction.Quantitative biology (Beijing, China) · 2023Article
- Article
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Authors and funding
5 authors.
Funding
Abstract
Elucidating the role of 3D architecture of DNA in gene regulation is crucial for understanding cell differentiation, tissue homeostasis and disease development. Among various chromatin conformation capture methods, HiChIP has received increasing attention for its significant improvement over other methods in profiling of regulatory (e.g. H3K27ac) and structural (e.g. cohesin) interactions. To facilitate the studies of 3D regulatory interactions, we developed a HiChIP interactions database, HiChIPdb (http://health.tsinghua.edu.cn/hichipdb/). The current version of HiChIPdb contains ∼262M annotated HiChIP interactions from 200 high-throughput HiChIP samples across 108 cell types. The functionalities of HiChIPdb include: (i) standardized categorization of HiChIP interactions in a hierarchical structure based on organ, tissue and cell line and (ii) comprehensive annotations of HiChIP interactions with regulatory genes and GWAS Catalog SNPs. To the best of our knowledge, HiChIPdb is the first comprehensive database that utilizes a unified pipeline to map the functional interactions across diverse cell types and tissues in different resolutions. We believe this database has the potential to advance cutting-edge research in regulatory mechanisms in development and disease by removing the barrier in data aggregation, preprocessing, and analysis.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.