Towards Personalized Epigenomics: Learning Shared Chromatin Landscapes and Joint De-Noising of Histone Modification Assays
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Epigenetic mechanisms enable cellular differentiation and the maintenance of distinct cell-types. They enable rapid responses to external signals through changes in gene regulation and their registration over longer time spans. Consequently, chromatin environments exhibit cell-type and individual specificity contributing to phenotypic diversity. Their genomic distributions are measured using ChIP-Seq and related methods. However, the chromatin landscape introduces significant biases into these measurements. Here, we introduce DecoDen to simultaneously learn shared chromatin landscapes while de-biasing individual measurement tracks. We demonstrate DecoDen’s effectiveness on an integrative analysis of histone modification patterns across multiple tissues in personal epigenomes.
