Abstract

   Reactome is an open-source, freely available database of human
   biological pathways and processes. A major goal of our work is to
   provide an integrated view of cellular signalling processes that spans
   from ligand–receptor interactions to molecular readouts at the level of
   metabolic and transcriptional events. To this end, we have built the
   first catalogue of all human G protein-coupled receptors (GPCRs) known
   to bind endogenous or natural ligands. The UniProt database has records
   for 797 proteins classified as GPCRs and sorted into families A/1, B/2
   and C/3 on the basis of amino accid sequence. To these records we have
   added details from the IUPHAR database and our own manual curation of
   relevant literature to create reactions in which 563 GPCRs bind ligands
   and also interact with specific G-proteins to initiate signalling
   cascades. We believe the remaining 234 GPCRs are true orphans. The
   Reactome GPCR pathway can be viewed as a detailed interactive diagram
   and can be exported in many forms. It provides a template for the
   orthology-based inference of GPCR reactions for diverse model organism
   species, and can be overlaid with protein–protein interaction and gene
   expression datasets to facilitate overrepresentation studies and other
   forms of pathway analysis.

   Database URL: [36]http://www.reactome.org

Introduction

   G protein-coupled receptors (GPCRs), also known as 7-transmembrane
   (7TM) domain receptors, comprise the largest and most diverse gene
   super-family in humans—>1% of the total protein-coding human genome.
   Estimates of the exact number of GPCR genes vary but a recent
   phylogenetic analysis identified over 800 ([37]1). Of these, 701 were
   classified within the rhodopsin family (type A) including 241
   non-olfactory receptors. Many protein coding genes are alternatively
   spliced giving rise to isoforms so the true number of functionally
   unique receptors may be much higher than estimates based on gene
   numbers.

   These GPCRs sense extracellular molecules and, through their
   interaction with G proteins, activate downstream signal transduction
   pathways. GPCRs respond to a huge range of stimuli, including light,
   odours, hormones, neurotransmitters and peptides ([38]2). GPCRs
   represent around half of cell surface drug targets ([39]3) and are a
   very successful therapeutic target family for the pharmaceutical
   industry accounting for the majority of best-selling drugs, ∼30% of all
   prescription pharmaceuticals on the market ([40]4). The potential for
   further exploitation remains high, as only 10% of GPCRs are targeted by
   these marketed drugs ([41]5).

   Reactome is a free, open-source pathways database. Information in
   Reactome is captured by expert curators and peer-reviewed by experts in
   their fields of biology. The data is extensively cross-referenced to
   databases such as Ensembl [[42]http://www.ensembl.org/index.html
   ([43]6)], GO [[44]http://www.ebi.ac.uk/QuickGO/ ([45]7)], PubMed
   ([46]http://www.ncbi.nlm.nih.gov/pubmed), ChEBI
   [[47]http://www.ebi.ac.uk/chebi/index.jsp ([48]8)], UniProt
   [[49]http://www.uniprot.org/ ([50]9)] and OMIM
   [[51]http://www.ncbi.nlm.nih.gov/omim ([52]10)]. Reactions for other
   species are inferred by orthology from curated human ones. Reactions
   can be viewed in the context of their pathways and interaction data can
   be overlaid to further expand the data richness. Tools are available in
   Reactome to help users with analyses such as pathway
   over-representation (enrichment) and pathway differential expression,
   and data including tables of pairwise protein–protein interactions
   computed from manually curated reactions and complexes can be
   downloaded in a range of formats.

   Several resources hold rich data for GPCRs. UniProt is a comprehensive
   protein knowledgebase of protein sequence and functional information.
   IUPHAR-db (International Union of basic and clinical PHARmacology,
   [53]http://www.iuphar-db.org/) is a database of receptor nomenclature
   and drug classification. Its GPCR section is arranged according to the
   sequence homology and functional similarity of these receptors. It also
   contains orphan GPCR lists. These resources were used as a starting
   point to catalogue the GPCR project in Reactome.

Materials and methods

   In UniProt, a query was constructed to search for all manually
   annotated and reviewed human GPCRs.

   Information in Reactome is annotated by database curators. These
   in-house experts systematically reviewed the literature for the three
   GPCR families. GPCRs whose ligands were identified from published
   experimental data were captured via the Curator Tool, an interface
   which allows the curator to annotate and structure data in accord with
   Reactome’s frame-based data model, and commit the results to a central
   repository ([54]11). Data was organized into the three main GPCR
   families, A/1, B/2 and C/3. Within each family, details were further
   structured based on the type of ligand. Attributes of a reaction
   captured by Reactome are:
     * input molecule(s)
     * output molecule(s)
     * catalyst (where appropriate)
     * compartment where reaction takes place
     * literature reference
     * species
     * links to preceding reactions (e.g. the causal connection between
       ligand binding and G-protein interaction)
     * membership in a pathway
     * text summary of reaction
     * curator
     * expert reviewer

   Input and output entities can be composed of proteins, simple chemicals
   or combinations of these entities (complexes).

   Useful information captured from IUPHAR-db by the curation team
   included:
     * the type of ligand the receptor bound, which helped in the
       organization of the project in Reactome. Ligands were represented
       if they are generally accepted in the literature to be the
       endogenous or natural ones
     * literature references associated with human receptors