Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlations
Abstract 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 accessibil...
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| Format: | Article |
| Language: | English |
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BMC
2024-12-01
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| Series: | Genome Biology |
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| Online Access: | https://doi.org/10.1186/s13059-024-03458-6 |
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| author | Xiaoyang Chen Keyi Li Xiaoqing Wu Zhen Li Qun Jiang Xuejian Cui Zijing Gao Yanhong Wu Rui Jiang |
| author_facet | Xiaoyang Chen Keyi Li Xiaoqing Wu Zhen Li Qun Jiang Xuejian Cui Zijing Gao Yanhong Wu Rui Jiang |
| author_sort | Xiaoyang Chen |
| collection | DOAJ |
| description | Abstract 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. |
| format | Article |
| id | doaj-art-0b31b3fde0db41f0a373a10f95276a32 |
| institution | Kabale University |
| issn | 1474-760X |
| language | English |
| publishDate | 2024-12-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj-art-0b31b3fde0db41f0a373a10f95276a322025-01-05T12:31:58ZengBMCGenome Biology1474-760X2024-12-0125112410.1186/s13059-024-03458-6Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlationsXiaoyang Chen0Keyi Li1Xiaoqing Wu2Zhen Li3Qun Jiang4Xuejian Cui5Zijing Gao6Yanhong Wu7Rui Jiang8Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua UniversityMinistry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua UniversityMinistry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua UniversityMinistry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua UniversityMinistry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua UniversityMinistry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua UniversityMinistry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua UniversityMinistry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua UniversityMinistry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua UniversityAbstract 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.https://doi.org/10.1186/s13059-024-03458-6Spatially variable peakSpatial ATAC-seqFeature selectionInter-cellular correlationsData imputationPeak module |
| spellingShingle | Xiaoyang Chen Keyi Li Xiaoqing Wu Zhen Li Qun Jiang Xuejian Cui Zijing Gao Yanhong Wu Rui Jiang Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlations Genome Biology Spatially variable peak Spatial ATAC-seq Feature selection Inter-cellular correlations Data imputation Peak module |
| title | Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlations |
| title_full | Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlations |
| title_fullStr | Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlations |
| title_full_unstemmed | Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlations |
| title_short | Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlations |
| title_sort | descart a method for detecting spatial chromatin accessibility patterns with inter cellular correlations |
| topic | Spatially variable peak Spatial ATAC-seq Feature selection Inter-cellular correlations Data imputation Peak module |
| url | https://doi.org/10.1186/s13059-024-03458-6 |
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