R&D Digital Technologies Department, Bayer AG, Berlin 13353, Germany.
Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany.
Nucleic Acids Res. 2022 Jan 7;50(D1):D587-D595. doi: 10.1093/nar/gkab1128.
Molecular interactions are key drivers of biological function. Providing interaction resources to the research community is important since they allow functional interpretation and network-based analysis of molecular data. ConsensusPathDB (http://consensuspathdb.org) is a meta-database combining interactions of diverse types from 31 public resources for humans, 16 for mice and 14 for yeasts. Using ConsensusPathDB, researchers commonly evaluate lists of genes, proteins and metabolites against sets of molecular interactions defined by pathways, Gene Ontology and network neighborhoods and retrieve complex molecular neighborhoods formed by heterogeneous interaction types. Furthermore, the integrated protein-protein interaction network is used as a basis for propagation methods. Here, we present the 2022 update of ConsensusPathDB, highlighting content growth, additional functionality and improved database stability. For example, the number of human molecular interactions increased to 859 848 connecting 200 499 unique physical entities such as genes/proteins, metabolites and drugs. Furthermore, we integrated regulatory datasets in the form of transcription factor-, microRNA- and enhancer-gene target interactions, thus providing novel functionality in the context of overrepresentation and enrichment analyses. We specifically emphasize the use of the integrated protein-protein interaction network as a scaffold for network inferences, present topological characteristics of the network and discuss strengths and shortcomings of such approaches.
分子相互作用是生物功能的关键驱动因素。向研究社区提供相互作用资源非常重要，因为它们允许对分子数据进行功能解释和基于网络的分析。共识路径数据库（ConsensusPathDB，http://consensuspathdb.org）是一个元数据库，它结合了来自人类的 31 个公共资源、16 个小鼠资源和 14 个酵母资源的多种类型的相互作用。研究人员通常使用 ConsensusPathDB 根据途径、基因本体论和网络邻域定义的分子相互作用集，评估基因、蛋白质和代谢物列表，并检索由多种相互作用类型形成的复杂分子邻域。此外，集成的蛋白质-蛋白质相互作用网络被用作传播方法的基础。在这里，我们展示了 ConsensusPathDB 的 2022 年更新，重点介绍了内容增长、附加功能和改进的数据库稳定性。例如，人类分子相互作用的数量增加到 859848 个，连接了 200499 个独特的物理实体，如基因/蛋白质、代谢物和药物。此外，我们以转录因子、microRNA 和增强子-基因靶相互作用的形式整合了调控数据集，从而在过表达和富集分析的背景下提供了新的功能。我们特别强调将集成的蛋白质-蛋白质相互作用网络用作网络推断的支架，展示网络的拓扑特征，并讨论此类方法的优缺点。
