Reactome-Recon lists

Reactome-Recon lists were generated automatically using a combination of two resources: the Reactome Neo4j graph database (Fabregat et al., 2018, PMID: 29377902) and the Recon Neo4j graph database (Balaur et al., 2017, PMID: 27993779) of the Human Metabolic Network Reconstruction Recon2 (Thiele et al., 2013, PMID: 23455439).

Reactome-Recon List 1 - Proteins

The list includes proteins from Recon2 that match those in Reactome pathways and participate in signalling processes in Reactome pathways as reactants or products, i.e. cases in which a protein is connected to a process via a production or consumption arc.

Reactome-Recon List 2 - Complexes

This list includes proteins from Recon2 that are also involved in complexes participating in signalling processes in Reactome pathways as reactants or products.

References

  1. Balaur I, Mazein A, Saqi M, Lysenko A, Rawlings CJ, Auffray C. Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks. Bioinformatics. 2017 Apr 1;33(7):1096-1098. doi: 10.1093/bioinformatics/btw731. PMID: 27993779.
  2. Fabregat A, Korninger F, Viteri G, Sidiropoulos K, Marin-Garcia P, Ping P, Wu G, Stein L, D’Eustachio P, Hermjakob H. Reactome graph database: Efficient access to complex pathway data. PLoS Comput Biol. 2018 Jan;14(1):e1005968. doi: 10.1371/journal.pcbi.1005968. PMID: 29377902.
  3. Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novère N, Malys N, Mazein A, Papin JA, Price ND, Selkov E, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BØ. A community-driven global reconstruction of human metabolism. Nat Biotechnol. 2013 May;31(5):419-25. doi: 10.1038/nbt.2488. PMID: 23455439.