The Reactome pathway knowledgebase

By A. Fabregat, S. Jupe, L. Matthews, K. Sidiropoulos, M. Gillespie, Maulik R. Kamdar, Phani V. Garapati, R. Haw, B. Jassal, Florian Korninger and 14 more. Nucleic Acids Res., 2013

4,899 citations recorded by the source corpus.

Reactome (http://www.reactome.org) is a manually curated open-source open-data resource of human pathways and reactions. The current version 46 describes 7088 human proteins (34% of the predicted human proteome), participating in 6744 reactions based on data extracted from 15 107 research publications with PubMed links. The Reactome Web site and analysis tool set have been completely redesigned to increase speed, flexibility and user friendliness. The data model has been extended to support annotation of disease processes due to infectious agents and to mutation.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/d8bd861b292233072aa40ab6bc029ac94d7f30af

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Citations in the corpus

Exploring Epigenomic Datasets by ChIPseeker (2022, methodology): “…DOSE (Yu, Wang, Yan, & He, 2015) for Disease Ontology analysis (Schriml et al., 2012); ReactomePA (Yu & He, 2016) for the Reactome pathway analysis (Croft et al., 2014); clusterProfiler (Wu, Xu, Guo, & Yu, 2021) for Gene Ontology (GO; Ashburner et al., 2000); and Kyoto Encyclopedia of Genes and…”
CD28 costimulation: from mechanism to therapy (2016, positive): “Differentially regulated genes were mapped to specific pathways (nodes), which are connected to each other based on common function (edges) according to the Reactome pathway database (Croft et al., 2014; Milacic et al., 2012).”
The Reactome pathway Knowledgebase (2015, methodology): “In Reactome, these processes are systematically described in molecular detail to generate an ordered network of molecular transformations, resulting in an extended version of a classic metabolic map described by a single, consistent data model (1).”
Updates in Rhea – an expert curated resource of biochemical reactions (2016, background): “Rhea also provides links to other metabolite and pathway databases such as KEGG (13), MetaCyc (14) and Reactome (15).”
HMDB 5.0: the Human Metabolome Database for 2022 (2021, background): “Unlike general metabolism or metabolic pathway databases such as KEGG (1), Reactome (2) and the Cyc databases (3) or general spectral databases such as the BioMagResBank (4), Metlin (5) or MassBank [https://massbank.”
The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets (2020, background): “These include pathways annotated in KEGG (41), Reactome (42) and Meta-Cyc (43), as well as protein complexes defined at the EBI Complex Portal (44) or by the Gene Ontology Consortium (45).”
Modelling local gene networks increases power to detect trans-acting genetic effects on gene expression (2016, result): “To objectively assess the associations retrieved by GNet-LMM and alternative methods, we tested to what extent the discovered trans eQTLs were consistent with Reactome pathways [41].”
KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis (2021, methodology): “In total, 5944 species were annotated with KEGG pathways, 41 species with PANTHER pathways, 14 species with Reactome pathways, 18 species with BioCyc pathways and 71 species with GO annotations (Table 1, Figure 3).”
Open Targets Platform: supporting systematic drug–target identification and prioritisation (2020, positive): “Many remain stable and provide constant updates for every one of our releases––such as ChEMBL (13), COSMIC (18), Reactome (19), ExpressionAtlas (20), Cancer Gene Census (21) or ePMC (22).”
g:Profiler—a web server for functional interpretation of gene lists (2016 update) (2016, positive): “For example, one may choose to only use biological processes of GO and Reactome pathways and filter out other databases and ontologies.”
The next-generation Open Targets Platform: reimagined, redesigned, rebuilt (2022, background): “Some of the data streams stem directly from public resources in our partner institutions (8–14).”