AtlasXplore: a web platform for visualizing and sharing spatial epigenome data.

MOTIVATION: In recent years, a growing number of spatial epigenome datasets have been generated, presenting rich opportunities for studying the regulation mechanisms in solid tissue sections. However, visual exploration of these datasets requires extensive computational processing of raw data, presenting a challenge for researchers without advanced computational skills to fully explore and analyze such datasets. RESULTS: Here, we introduce AtlasXplore, a web-based platform that enables scientists to interactively navigate a growing collection of spatial epigenome data using an expanding set of tools. AVAILABILITY AND IMPLEMENTATION: https://web.atlasxomics.com.

Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data.

Single-cell RNA sequencing (scRNA-seq) provides unique insights into the pathology and cellular origin of disease. We introduce single-cell disease relevance score (scDRS), an approach that links scRNA-seq with polygenic disease risk at single-cell resolution, independent of annotated cell types. scDRS identifies cells exhibiting excess expression across disease-associated genes implicated by genome-wide association studies (GWASs). We applied scDRS to 74 diseases/traits and 1.3 million single-cell gene-expression profiles across 31 tissues/organs. Cell-type-level results broadly recapitulated known cell-type-disease associations. Individual-cell-level results identified subpopulations of disease-associated cells not captured by existing cell-type labels, including T cell subpopulations associated with inflammatory bowel disease, partially characterized by their effector-like states; neuron subpopulations associated with schizophrenia, partially characterized by their spatial locations; and hepatocyte subpopulations associated with triglyceride levels, partially characterized by their higher ploidy levels. Genes whose expression was correlated with the scDRS score across cells (reflecting coexpression with GWAS disease-associated genes) were strongly enriched for gold-standard drug target and Mendelian disease genes.