Pathway annotation and analysis with Reactome: The solute carrier class of membrane transporters

Reactome (http://www.reactome.org webcite) is a freely available and open-source database of biological pathways [1,2]. Expert scientists curate information into Reactome, which is then peer-reviewed to obtain a consensus representation of the process or pathway. The data are extensively cross-linked to major protein and nucleotide sequence databases, as well as to the Gene Ontology and PubMed databases. A new website for Reactome was recently released. This includes new functionality for interacting with curated pathways and analysing them with linked or user-supplied datasets. Tools in this new version of Reactome allow users to overlay interaction or expression data, further enriching the pathway information. The results of these analyses can then be downloaded in a range of formats.We have recently completed a catalogue of the solute carrier (SLC) class of transmembrane transporters. These proteins are well conserved in all eukaryotes, as well as most prokaryotes, and play a gate-keeping role for cells and organelles, controlling the uptake and efflux of many types of substrates, such as sugars, inorganic cations and anions, organic anions and carboxylates, amino acids and oligopeptides, fatty acids and lipids, and neurotrans-mitters and vitamins. The SLC superfamily comprises 55 gene families, with 362 putatively functional protein-coding genes reported [3,4]. Of these, 231 with the criterion that the transporter has a substrate which it transports across the membrane have been catalogued in Reactome. The remainder are orphan proteins, with no characterised substrates at this time. This pathway will be used as the basis for describing the use of Reactome's analysis tools.Reactome's website can be viewed on PCs, Macs or Linux computers with later versions of the Internet Explorer (IE), Firefox or Safari browsers. Reactome's whole content can be downloaded as a mysql datadump (http://www.reactome.org/download/index.html webcite). Other Reactome datasets and code