Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Department of Operations and Decision Systems, Université Laval, Quebec, Canada.
BMC Bioinformatics. 2023 Jun 7;24(1):240. doi: 10.1186/s12859-023-05340-x.
Protein-DNA binding sites of ChIP-seq experiments are identified where the binding affinity is significant based on a given threshold. The choice of the threshold is a trade-off between conservative region identification and discarding weak, but true binding sites.
We rescue weak binding sites using MSPC, which efficiently exploits replicates to lower the threshold required to identify a site while keeping a low false-positive rate, and we compare it to IDR, a widely used post-processing method for identifying highly reproducible peaks across replicates. We observe several master transcription regulators (e.g., SP1 and GATA3) and HDAC2-GATA1 regulatory networks on rescued regions in K562 cell line.
We argue the biological relevance of weak binding sites and the information they add when rescued by MSPC. An implementation of the proposed extended MSPC methodology and the scripts to reproduce the performed analysis are freely available at https://genometric.github.io/MSPC/ ; MSPC is distributed as a command-line application and an R package available from Bioconductor ( https://doi.org/doi:10.18129/B9.bioc.rmspc ).
ChIP-seq 实验中的蛋白质-DNA 结合位点是根据给定的阈值确定的，其结合亲和力具有显著意义。阈值的选择是在保守区域识别和丢弃弱但真实的结合位点之间的权衡。
我们使用 MSPC 来挽救弱结合位点，该方法有效地利用重复来降低识别位点所需的阈值，同时保持低的假阳性率，我们将其与 IDR 进行比较，IDR 是一种广泛用于识别重复中高度可重复峰的后处理方法。我们观察到在 K562 细胞系的挽救区域中存在几个主转录调控因子（如 SP1 和 GATA3）和 HDAC2-GATA1 调控网络。
我们认为弱结合位点的生物学相关性以及通过 MSPC 挽救时它们所提供的信息是重要的。拟议的扩展 MSPC 方法的实现和用于重现执行的分析的脚本可在 https://genometric.github.io/MSPC/ 上免费获得；MSPC 作为命令行应用程序和来自 Bioconductor 的 R 包分发（https://doi.org/doi:10.18129/B9.bioc.rmspc）。
