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Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlations

by Jiang, Qun , Cui, Xuejian , Li, Zhen , Wu, Yanhong , Gao, Zijing , Li, Keyi , Chen, Xiaoyang , Wu, Xiaoqing , Jiang, Rui

in Animal Genetics and Genomics / Animals / Bioinformatics / Biomedical and Life Sciences / Cell Communication / Chromatin / Chromatin - genetics / Clustering / Data analysis / Data imputation / Datasets as Topic / epigenome / Evolutionary Biology / Feature selection / Gene Expression / Genomics / Human Genetics / Humans / Inter-cellular correlations / landscapes / Life Sciences / Melanoma - genetics / Melanoma - pathology / Method / Methods / Mice / Microbial Genetics and Genomics / Neoplasm Metastasis / Peak module / Plant Genetics and Genomics / Spatial ATAC-seq / Spatial variability / Spatially variable peak

2024

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Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlations

by Jiang, Qun , Cui, Xuejian , Li, Zhen , Wu, Yanhong , Gao, Zijing , Li, Keyi , Chen, Xiaoyang , Wu, Xiaoqing , Jiang, Rui

2024

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Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlations

by Jiang, Qun , Cui, Xuejian , Li, Zhen , Wu, Yanhong , Gao, Zijing , Li, Keyi , Chen, Xiaoyang , Wu, Xiaoqing , Jiang, Rui

2024

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Journal Article

Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlations

Jiang, Qun,

Cui, Xuejian,

Li, Zhen,

Wu, Yanhong,

Gao, Zijing,

Li, Keyi,

Chen, Xiaoyang,

Wu, Xiaoqing,

Jiang, Rui

2024

Overview

Spatial epigenomic technologies enable simultaneous capture of spatial location and chromatin accessibility of cells within tissue slices. Identifying peaks that display spatial variation and cellular heterogeneity is the key analytic task for characterizing the spatial chromatin accessibility landscape of complex tissues. Here, we propose an efficient and iterative model, Descart, for spatially variable peaks identification based on the graph of inter-cellular correlations. Through the comprehensive benchmarking, we demonstrate the superiority of Descart in revealing cellular heterogeneity and capturing tissue structure. Utilizing the graph of inter-cellular correlations, Descart shows its potential to denoise data, identify peak modules, and detect gene-peak interactions.

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Publisher

BioMed Central,Springer Nature B.V,BMC

Subject

Animal Genetics and Genomics

/ Animals

/ Bioinformatics

/ Biomedical and Life Sciences

/ Cell Communication

/ Chromatin

/ Chromatin - genetics