Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA, 02142, USA.
Howard Hughes Medical Institute, Cambridge, MA, 02142, USA.
BMC Bioinformatics. 2023 May 12;24(1):195. doi: 10.1186/s12859-023-05306-z.
One strategy for identifying targets of a regulatory factor is to perturb the factor and use high-throughput RNA sequencing to examine the consequences. However, distinguishing direct targets from secondary effects and experimental noise can be challenging when confounding signal is present in the background at varying levels.
Here, we present a statistical modeling strategy to identify microRNAs that are primary substrates of target-directed miRNA degradation (TDMD) mediated by ZSWIM8. This method uses a bi-beta-uniform mixture (BBUM) model to separate primary from background signal components, leveraging the expectation that primary signal is restricted to upregulation and not downregulation upon loss of ZSWIM8. The BBUM model strategy retained the apparent sensitivity and specificity of the previous ad hoc approach but was more robust against outliers, achieved a more consistent stringency, and could be performed using a single cutoff of false discovery rate (FDR).
We developed the BBUM model, a robust statistical modeling strategy to account for background secondary signal in differential expression data. It performed well for identifying primary substrates of TDMD and should be useful for other applications in which the primary regulatory targets are only upregulated or only downregulated. The BBUM model, FDR-correction algorithm, and significance-testing methods are available as an R package at https://github.com/wyppeter/bbum .
鉴定调控因子靶标的策略之一是扰动该因子，然后使用高通量 RNA 测序来检测后果。然而，当背景中存在不同水平的混杂信号时，区分直接靶标和次级效应以及实验噪声可能具有挑战性。
在这里，我们提出了一种统计建模策略，用于鉴定被 ZSWIM8 介导的靶向 miRNA 降解（TDMD）的 miRNA 作为主要底物。该方法使用双-β均匀混合（BBUM）模型来分离主要信号和背景信号成分，利用这样的期望，即在 ZSWIM8 缺失时，主要信号仅限于上调而不是下调。BBUM 模型策略保留了先前特定方法的明显灵敏度和特异性，但对离群值更稳健，实现了更一致的严格性，并且可以使用单个错误发现率（FDR）的截止值进行。
我们开发了 BBUM 模型，这是一种稳健的统计建模策略，可以解释差异表达数据中的背景二级信号。它在鉴定 TDMD 的主要底物方面表现良好，并且应该对其他仅上调或仅下调主要调控靶点的应用有用。BBUM 模型、FDR 校正算法和显著性检验方法可在 https://github.com/wyppeter/bbum 上获得。
