Sorokina Oksana, Sorokin Anatoly, Armstrong J Douglas
School of informatics, University of Edinburgh, Edinburgh EH8 9AB, UK.
Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK.
Bioinform Adv. 2022 Nov 12;2(1):vbac086. doi: 10.1093/bioadv/vbac086. eCollection 2022.
The neuronal synapse is underpinned by a large and diverse proteome but the molecular evidence is spread across many primary datasets. These data were recently curated into a single dataset describing a landscape of ∼8000 proteins found in studies of mammalian synapses. Here, we describe programmatic access to the dataset via the R/Bioconductor package Synaptome.db, which enables convenient and in-depth data analysis from within the Bioconductor environment. Synaptome.db allows users to obtain the respective gene information, e.g. subcellular localization, brain region, gene ontology, disease association and construct custom protein-protein interaction network models for gene sets and entire subcellular compartments.
The package Synaptome.db is part of Bioconductor since release 3.14, https://bioconductor.org/packages/release/data/annotation/html/synaptome.db.html, it is open source and available under the Artistic license 2.0. The development version is maintained on GitHub (https://github.com/lptolik/synaptome.db). Full documentation including examples is provided in the form of vignettes on the package webpage.
Supplementary data are available at online.
神经元突触由庞大且多样的蛋白质组支撑，但分子证据分散在许多原始数据集中。这些数据最近被整理成一个单一数据集，描述了在哺乳动物突触研究中发现的约8000种蛋白质的情况。在这里，我们描述了通过R/Bioconductor包Synaptome.db对该数据集进行编程访问的方法，这使得在Bioconductor环境中能够方便地进行深入数据分析。Synaptome.db允许用户获取各自的基因信息，例如亚细胞定位、脑区、基因本体、疾病关联，并为基因集和整个亚细胞区室构建自定义的蛋白质-蛋白质相互作用网络模型。
自版本3.14起，Synaptome.db包是Bioconductor的一部分，网址为https://bioconductor.org/packages/release/data/annotation/html/synaptome.db.html，它是开源的，根据艺术许可2.0提供。开发版本在GitHub上维护（https://github.com/lptolik/synaptome.db）。完整的文档包括示例，以包网页上的小插图形式提供。
补充数据可在网上获取。
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