title: Pathway annotation and analysis with Reactome: the solute carrier class of membrane transporters.
abstract: Reactome is an expert-authored, peer-reviewed knowledge base of human reactions and pathways that functions as a data-mining resource and electronic textbook. Its current release covers approximately 23 per cent of the complete human proteome from UniProt. The pathway browser, search and data-mining tools facilitate searching and visualising pathway data and the analysis of user-supplied high-throughput datasets. A catalogue of all the solute-carrier (SLC) class of transporters which have known ligands has been annotated in Reactome. Reactome provides a detailed and interactive view of this set of transport reactions. Using the example of the SLC class of transporters, we show how they can be overlaid with protein-protein interaction, protein-drug interaction and gene expression data and compared with equivalent pathways in other species, to facilitate over-representation, expression and other pathway analyses.
authors.affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. bj1@ebi.ac.uk
authors.forename: Bijay
authors.initials: B
authors.lastname: Jassal
mesh_terms: D053898:Biosynthetic Pathways / Q000235:genetics*; D030562:Databases, Protein; D006801:Humans; D051188:Knowledge Bases; D026901:Membrane Transport Proteins / Q000145:classification* / Q000235:genetics / Q000378:metabolism*; D058977:Molecular Sequence Annotation / Q000379:methods*; D011485:Protein Binding; D020543:Proteome / Q000235:genetics*
chemical_list: D026901:Membrane Transport Proteins; D020543:Proteome