Single-cell gene regulation network inference by large-scale data integration.
Single-cell gene regulation network inference by large-scale data integration.
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DOI：
10.1093/nar/gkac819
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发表时间：
2022-11-28
影响因子：
14.9
通讯作者：
Wang, Chenfei
中科院分区：
文献类型：
--
作者：
Dong, Xin;Tang, Ke;Xu, Yunfan;Wei, Hailin;Han, Tong;Wang, Chenfei
单细胞ATAC-seq （scATAC-seq）已被证明是研究单细胞水平基因调控的最先进方法。然而，现有的方法不能精确地揭示细胞类型特异性的转录调控因子（TRs）结合，并在单细胞中构建基因调控网络（grn）。在过去的几十年里，ChIP-seq被广泛用于分析TR结合位点。在这里，我们开发了SCRIP，这是一种基于scATAC-seq和大规模TR ChIP-seq参考文献集成的推断单细胞TR活性和靶标的综合方法。与现有的基于基序的方法相比，我们的方法在评估TR结合活性方面表现出更高的性能，并且与匹配的TR表达具有更高的一致性。此外，我们的方法能够识别TR靶基因，并基于调控电位模型在单细胞分辨率上构建grn。我们证明了SCRIP在精确的细胞类型聚类、谱系追踪和推断多种生物系统中细胞类型特异性grn方面的效用。SCRIP可在https://github.com/wanglabtongji/SCRIP免费获得。
Single-cell ATAC-seq (scATAC-seq) has proven to be a state-of-art approach to investigating gene regulation at the single-cell level. However, existing methods cannot precisely uncover cell-type-specific binding of transcription regulators (TRs) and construct gene regulation networks (GRNs) in single-cell. ChIP-seq has been widely used to profile TR binding sites in the past decades. Here, we developed SCRIP, an integrative method to infer single-cell TR activity and targets based on the integration of scATAC-seq and a large-scale TR ChIP-seq reference. Our method showed improved performance in evaluating TR binding activity compared to the existing motif-based methods and reached a higher consistency with matched TR expressions. Besides, our method enables identifying TR target genes as well as building GRNs at the single-cell resolution based on a regulatory potential model. We demonstrate SCRIP’s utility in accurate cell-type clustering, lineage tracing, and inferring cell-type-specific GRNs in multiple biological systems. SCRIP is freely available at https://github.com/wanglabtongji/SCRIP.
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影响因子：
46.9
作者：
Ernst J;Kellis M
通讯作者：
Kellis M
DOI：
10.1073/pnas.1205834109
发表时间：
2012-05-29
影响因子：
11.1
作者：
Bollig, Nadine;Bruestle, Anne;Lohoff, Michael
通讯作者：
Lohoff, Michael
影响因子：
5.8
作者：
Angerer, Philipp;Haghverdi, Laleh;Buettner, Florian
通讯作者：
Buettner, Florian
单细胞染色质可及性揭示了调节变化的原理。
影响因子：
64.8
作者：
Buenrostro JD;Wu B;Litzenburger UM;Ruff D;Gonzales ML;Snyder MP;Chang HY;Greenleaf WJ
通讯作者：
Greenleaf WJ
影响因子：
64.5
作者：
Hainer, Sarah J.;Boskovic, Ana;Fazzio, Thomas G.
通讯作者：
Fazzio, Thomas G.