ArticleNucleic acids research2024
ChIP-Atlas 3.0: a data-mining suite to explore chromosome architecture together with large-scale regulome data.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 144 papers, 2 of them syntheses that pooled it.
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Who cites it
144 citing papers in PubMed, 2 syntheses or guidelines pooled it.
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- Deciphering cell-type-and temporally specific matrisome expression signatures in human cortical development and neurodevelopmental disorders via scRNA-seq meta-analysis.Nature communications · 2025Pooled it
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- Uncovering pan-cancer signatures of chemoresistance.Genome medicine · 2026Article
- GLM-Prior: a genomic language model for transferable sequence-derived priors in gene regulatory network inference.Nature communications · 2026Article
- A transcription factor regulatory atlas for activity inference and perturbation prediction.Nucleic acids research · 2026Article
- Benchmarking methods for inferring single-cell transcription factor activity using large-scale perturbation sequencing data.Briefings in bioinformatics · 2026Article
- IL1RAP Antibody-Drug Conjugates Potently Target Primary and Metastatic Diseases in Multiple Oncofusion-Driven Cancers.Cancer discovery · 2026Article
- Advances in genomics-driven genetic decoding and genomic design breeding in tomato.Horticulture research · 2026Article
- Altered bone marrow niche forms central innate immune memory driving cardiac dysfunction.Nature communications · 2026Article
- Non-canonical NF-κB drives a fate switch from germinal center to early effector B cells.iScience · 2026Article
- An Isogenic Yeast Model Reveals the Influence of Native Promoter G‑Quadruplex Forming Sequences on P53 and NF-κB Transactivation.ACS bio & med chem Au · 2026Article
- Injury-driven stromal exhaustion disrupts intrinsic regenerative capability.Nature communications · 2026Article
- A long first intron of PROS1 modulates protein S expression across tissues in mice and humans.Blood advances · 2026Article
84 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
ChIP-Atlas (https://chip-atlas.org/) presents a suite of data-mining tools for analyzing epigenomic landscapes, powered by the comprehensive integration of over 376 000 public ChIP-seq, ATAC-seq, DNase-seq and Bisulfite-seq experiments from six representative model organisms. To unravel the intricacies of chromatin architecture that mediates the regulome-initiated generation of transcriptional and phenotypic diversity within cells, we report ChIP-Atlas 3.0 that enhances clarity by incorporating additional tracks for genomic and epigenomic features within a newly consolidated 'annotation track' section. The tracks include chromosomal conformation (Hi-C and eQTL datasets), transcriptional regulatory elements (ChromHMM and FANTOM5 enhancers), and genomic variants associated with diseases and phenotypes (GWAS SNPs and ClinVar variants). These annotation tracks are easily accessible alongside other experimental tracks, facilitating better elucidation of chromatin architecture underlying the diversification of transcriptional and phenotypic traits. Furthermore, 'Diff Analysis,' a new online tool, compares the query epigenome data to identify differentially bound, accessible, and methylated regions using ChIP-seq, ATAC-seq and DNase-seq, and Bisulfite-seq datasets, respectively. The integration of annotation tracks and the Diff Analysis tool, coupled with continuous data expansion, renders ChIP-Atlas 3.0 a robust resource for mining the landscape of transcriptional regulatory mechanisms, thereby offering valuable perspectives, particularly for genetic disease research and drug discovery.
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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.