BioQuant, Heidelberg University, 69120 Heidelberg, Germany.
Biochemistry Center (BZH), Heidelberg University, 69120 Heidelberg, Germany.
Nucleic Acids Res. 2024 Jul 5;52(W1):W333-W340. doi: 10.1093/nar/gkae423.
Protein-protein interaction experiments still yield many false positive interactions. The socioaffinity metric can distinguish true protein-protein interactions from noise based on available data. Here, we present WeSA (Weighted SocioAffinity), which considers large datasets of interaction proteomics data (IntAct, BioGRID, the BioPlex) to score human protein interactions and, in a statistically robust way, flag those (even from a single experiment) that are likely to be false positives. ROC analysis (using CORUM-PDB positives and Negatome negatives) shows that WeSA improves over other measures of interaction confidence. WeSA shows consistently good results over all datasets (up to: AUC = 0.93 and at best threshold: TPR = 0.84, FPR = 0.11, Precision = 0.98). WeSA is freely available without login (wesa.russelllab.org). Users can submit their own data or look for organized information on human protein interactions using the web server. Users can either retrieve available information for a list of proteins of interest or calculate scores for new experiments. The server outputs either pre-computed or updated WeSA scores for the input enriched with information from databases. The summary is presented as a table and a network-based visualization allowing the user to remove those nodes/edges that the method considers spurious.
蛋白质-蛋白质相互作用实验仍然会产生许多假阳性相互作用。社会亲和度度量可以根据现有数据将真实的蛋白质-蛋白质相互作用与噪声区分开来。在这里，我们提出了 WeSA（加权社会亲和度），它考虑了大量的相互作用蛋白质组学数据集（IntAct、BioGRID、BioPlex）来评分人类蛋白质相互作用，并以统计上稳健的方式标记那些（即使来自单个实验）可能是假阳性的相互作用。ROC 分析（使用 CORUM-PDB 阳性和 Negatome 阴性）表明，WeSA 优于其他相互作用置信度度量。WeSA 在所有数据集上都表现出一致的良好结果（最高可达：AUC=0.93，最佳阈值时：TPR=0.84，FPR=0.11，Precision=0.98）。WeSA 无需登录即可免费使用（wesa.russelllab.org）。用户可以提交自己的数据，也可以使用网络服务器查找有关人类蛋白质相互作用的组织信息。用户可以检索感兴趣的蛋白质列表的可用信息，也可以计算新实验的分数。服务器会输出预先计算或更新的 WeSA 分数，这些分数是通过数据库信息丰富输入而得到的。摘要以表格和基于网络的可视化形式呈现，允许用户删除该方法认为是虚假的节点/边。
