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ChIP-Atlas integrates epigenomic data to enhance analysis and data reliability in multicellular organisms, highlighting advancements.
ChIP-Atlas (https://chip-atlas.org/) is a data-mining platform that systematically processes and integrates public epigenomic profiling data, including ChIP-seq, ATAC-seq, DNase-seq, and Bisulfite-seq, together with curated sample metadata, currently encompassing >460 000 experiments across multiple model organisms. In this 2025 update, an experiment-level quality control framework was embedded in every experiment page, enabling intuitive assessment of data reliability and representativeness. In addition, a parametric analysis of gene set enrichment-based module was implemented, allowing enrichment analysis directly from continuous RNA-seq count tables without relying on threshold-defined, discrete gene lists, thereby helping elucidate underlying gene regulatory mechanisms. Combined with sustained data expansion, these updates advance ChIP-Atlas into a more quantitative and flexible platform for exploring the epigenomic landscape in multicellular organisms, marking its 10th anniversary.
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Zou et al. (2026) studied this question.
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