Synaptome.db: a bioconductor package for analysis of synaptic proteomics data

Author(s): Dr Oksana Sorokina,Anatoly Sorokin,J Douglas Armstrong

Affiliation(s): University of Edinburgh



The neuronal synapse is underpinned by a large and diverse proteome with the molecular evidence spread across many primary datasets. Recently, we curated them into a single database describing a landscape of ∼8000 proteins found in studies of mammalian synapses [1]. We provide the programmatic access to the database via package Synaptome.db, which enables convenient and in-depth data analysis within the Bioconductor environment. Synaptome.db functionality allow users to obtain the respective gene information, e.g. subcellular localization (presynaptic, postsynaptic, synaptic vesicle, synaptosome), brain region, gene ontology and disease association. It supports extraction of the protein population of entire subcellular compartment and/or brain region, enabling custom filters for the proteins that were identified more frequently than others, and, thus, may correspond to more probable synaptic residents. Moreover, given the availability of the protein-protein interaction data in the same data source, package allows reconstruction of custom protein–protein interaction network models for gene sets and entire subcellular compartments or brain regions, which can be further analysed with respect to functionality and diseases [2]. [1] Sorokina, O, et al. A unified resource and configurable model of the synapse proteome and its role in disease. Scientific reports 11 (1), 9967 [2] Sorokina, O, Sorokin, A, Armstrong JD. Synaptome. db: a bioconductor package for synaptic proteomics data. Bioinformatics Advances 2 (1), vbac086