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Context-specific interactions in literature-curated protein interaction databases

机译：文献策蛋白互动数据库中的上下文特异性相互作用

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Databases of literature-curated protein-protein interactions (PPIs) are often used to interpret high-throughput interactome mapping studies and estimate error rates. These databases combine interactions across thousands of published studies and experimental techniques. Because the tendency for two proteins to interact depends on the local conditions, this heterogeneity of conditions means that only a subset of database PPIs are interacting during any given experiment. A typical use of these databases as gold standards in interactome mapping projects, however, assumes that PPIs included in the database are indeed interacting under the experimental conditions of the study. Using raw data from 20 co-fractionation experiments and six published interactomes, we demonstrate that this assumption is often false, with up to 55% of purported gold standard interactions showing no evidence of interaction, on average. We identify a subset of CORUM database complexes that do show consistent evidence of interaction in co-fractionation studies, and we use this subset as gold standards to dramatically improve interactome mapping as judged by the number of predicted interactions at a given error rate. We recommend using this CORUM subset as the gold standard set in future co-fractionation studies. More generally, we recommend using the subset of literature-curated PPIs that are specific to the experimental context whenever possible.
机译：文献型蛋白质 - 蛋白质相互作用（PPI）的数据库通常用于解释高通量互乱映射研究和估计误差速率。这些数据库结合了数千名发布研究和实验技术的互动。因为两种蛋白质的趋势取决于局部条件，所以这种条件的这种异质性意味着在任何给定的实验期间，只有数据库PPI的子集是相互作用。然而，典型使用这些数据库作为互乱映射项目中的黄金标准，假定数据库中包含的PPI确实在研究的实验条件下进行交互。使用来自20个共分的实验和六个公布的杂志的原始数据，我们证明了这种假设通常是假的，最高可达55％的声称金标准相互作用，显示没有相互作用的依据。我们识别Corum数据库复合体的子集，该组件确实显示了共分馏研究中的相互作用的一致证据，我们将该子集用作金标准，以显着改善通过以给定错误率的预测交互的数量判断的互乱映射。我们建议使用此Corum子集作为未来共分分类研究中的黄金标准集。更一般地，我们建议使用特定于实验上下文的文献策划PPI的子集。

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