sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network.
sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network.
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DOI：
10.1038/s41540-022-00245-6
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发表时间：
2022-09-12
影响因子：
4
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中科院分区：
文献类型：
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单细胞技术的繁荣带来了来自不同来源的高维数据的激增，这些数据从不同的角度代表了蜂窝系统。随着这些单细胞技术的进步，跨模式整合单细胞数据成为一个新的计算挑战。在这里，我们提出了一种对抗性的方法，sciCAN，以无监督的方式整合单细胞染色质可及性和基因表达数据。我们在5个scATAC-seq/scRNA-seq数据集中用5种现有方法对sciCAN进行了基准测试，证明了我们的方法处理数据集成时，在数据集之间具有一致的性能，并且比其他5种现有方法更好地平衡了模态之间的相互传输。我们进一步将sciCAN应用于10 X Multiome数据，并证实了集成表示保留了造血层次内的生物学关系。最后，我们研究了CRISPR干扰的单细胞K562 ATAC-seq和RNA-seq数据，以识别对这些不同模式的不同干扰具有相关响应的细胞。
The boom in single-cell technologies has brought a surge of high dimensional data that come from different sources and represent cellular systems from different views. With advances in these single-cell technologies, integrating single-cell data across modalities arises as a new computational challenge. Here, we present an adversarial approach, sciCAN, to integrate single-cell chromatin accessibility and gene expression data in an unsupervised manner. We benchmarked sciCAN with 5 existing methods in 5 scATAC-seq/scRNA-seq datasets, and we demonstrated that our method dealt with data integration with consistent performance across datasets and better balance of mutual transferring between modalities than the other 5 existing methods. We further applied sciCAN to 10X Multiome data and confirmed that the integrated representation preserves biological relationships within the hematopoietic hierarchy. Finally, we investigated CRISPR-perturbed single-cell K562 ATAC-seq and RNA-seq data to identify cells with related responses to different perturbations in these different modalities.
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影响因子：
46.9
作者：
Becht, Etienne;McInnes, Leland;Newell, Evan W.
通讯作者：
Newell, Evan W.
影响因子：
46.9
作者：
Lin, Yingxin;Wu, Tung-Yu;Wan, Sheng;Yang, Jean Y. H.;Wong, Wing H.;Wang, Y. X. Rachel
通讯作者：
Wang, Y. X. Rachel
影响因子：
30.8
作者：
Corces, M. Ryan;Buenrostro, Jason D.;Wu, Beijing;Greenside, Peyton G.;Chan, Steven M.;Koenig, Julie L.;Snyder, Michael P.;Pritchard, Jonathan K.;Kundaje, Anshul;Gkeenleaf, William J.;Majeti, Ravindra;Chang, Howard Y.
通讯作者：
Chang, Howard Y.
影响因子：
64.5
作者：
Dixit, Atray;Pamas, Oren;Li, Biyu;Chen, Jenny;Fulco, Charles P.;Jerby-Amon, Livnat;Marjanovic, Nemanja D.;Dionne, Danielle;Burks, Tyler;Raychowdhury, Raktima;Adamson, Britt;Norman, Thomas M.;Lander, Eric S.;Weissman, Jonathan S.;Friedman, Nir;Regev, Aviv
通讯作者：
Regev, Aviv
影响因子：
64.8
作者：
La Manno G;Soldatov R;Zeisel A;Braun E;Hochgerner H;Petukhov V;Lidschreiber K;Kastriti ME;Lönnerberg P;Furlan A;Fan J;Borm LE;Liu Z;van Bruggen D;Guo J;He X;Barker R;Sundström E;Castelo-Branco G;Cramer P;Adameyko I;Linnarsson S;Kharchenko PV
通讯作者：
Kharchenko PV