UCSC Genomics Institute, Biomolecular Engineering, University of California, Santa Cruz, USA.
Genome Biol. 2024 Aug 14;25(1):220. doi: 10.1186/s13059-024-03368-7.
Inferring gene regulatory networks from single-cell RNA-sequencing trajectories has been an active area of research yet methods are still needed to identify regulators governing cell transitions. We developed DREAMIT (Dynamic Regulation of Expression Across Modules in Inferred Trajectories) to annotate transcription-factor activity along single-cell trajectory branches, using ensembles of relations to target genes. Using a benchmark representing several different tissues, as well as external validation with ATAC-Seq and Perturb-Seq data on hematopoietic cells, the method was found to have higher tissue-specific sensitivity and specificity over competing approaches.
从单细胞 RNA 测序轨迹推断基因调控网络一直是一个活跃的研究领域，但仍需要方法来识别控制细胞转变的调节剂。我们开发了 DREAMIT（推断轨迹中模块表达的动态调控），使用针对靶基因的关系集合来注释转录因子沿着单细胞轨迹分支的活性。使用代表几种不同组织的基准以及对造血细胞的 ATAC-Seq 和 Perturb-Seq 数据的外部验证，该方法在组织特异性敏感性和特异性方面优于竞争方法。
