Pathway annotation and analysis with Reactome: The solute carrier class of membrane transporters
Tóm tắt
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.
Tài liệu tham khảo
Vastrik I, D'Eustachio P, Schmidt E, Gopinath G, et al: Reactome: A knowledge base of biologic pathways and processes. Genome Biol. 2007, 8: R39-10.1186/gb-2007-8-3-r39.
Matthews L, Gopinath G, Gillespie M, Caudy M, et al: Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 2009, 37: D619-D622. 10.1093/nar/gkn863.
Hediger MA, Romero MF, Peng JB, Rolfs A, et al: The ABCs of solute carriers: Physiological, pathological and therapeutic implications of human membrane transport proteins Introduction. Pflugers Arch. 2004, 447: 465-468. 10.1007/s00424-003-1192-y.
He L, Vasiliou K, Nebert DW: Analysis and update of the human solute carrier (SLC) gene superfamily. Hum Genomics. 2009, 3: 195-206.
UniProt Consortium: The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res. 2010, 38: D142-D148.
Aranda B, Achuthan P, Alam-Faruque Y, Armean I, et al: The IntAct molecular interaction database in 2010. Nucleic Acids Res. 2009, 38: D525-D531.
Kapushesky M, Emam I, Holloway E, Kurnosov P, et al: Gene expression atlas at the European bioinformatics institute. Nucleic Acids Res. 2010, 38: D690-D698. 10.1093/nar/gkp936.