The reactome pathway knowledgebase 2022.

Journal: Nucleic acids research
PMID: 34788843

Abstract

The Reactome Knowledgebase (https://reactome.org), an Elixir core resource, provides manually curated molecular details across a broad range of physiological and pathological biological processes in humans, including both hereditary and acquired disease processes. The processes are annotated as an ordered network of molecular transformations in a single consistent data model. Reactome thus functions both as a digital archive of manually curated human biological processes and as a tool for discovering functional relationships in data such as gene expression profiles or somatic mutation catalogs from tumor cells. Recent curation work has expanded our annotations of normal and disease-associated signaling processes and of the drugs that target them, in particular infections caused by the SARS-CoV-1 and SARS-CoV-2 coronaviruses and the host response to infection. New tools support better simultaneous analysis of high-throughput data from multiple sources and the placement of understudied ('dark') proteins from analyzed datasets in the context of Reactome's manually curated pathways.

Authors

  • Marc Gillespie
    Ontario Institute for Cancer Research, Toronto, ON, M5G 0A3, Canada.
  • Bijay Jassal
    Ontario Institute for Cancer Research, Toronto, ON, Canada.
  • Ralf Stephan
    Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
  • Marija Milacic
    Ontario Institute for Cancer Research, Toronto, ON, M5G 0A3, Canada.
  • Karen Rothfels
    Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
  • Andrea Senff-Ribeiro
    Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
  • Johannes Griss
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria.
  • Cristoffer Sevilla
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
  • Lisa Matthews
    Department of Biochemistry & Molecular Pharmacology, NYU. Langone Medical Center, New York, NY, United States.
  • Chuqiao Gong
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
  • Chuan Deng
    Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and telecommunications, Chongqing, China.
  • Thawfeek Varusai
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Eliot Ragueneau
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
  • Yusra Haider
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
  • Bruce May
    Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
  • Veronica Shamovsky
    Department of Biochemistry & Molecular Pharmacology, NYU School of Medicine, New York, New York, United States of America.
  • Joel Weiser
    Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
  • Timothy Brunson
    Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, 97239, USA.
  • Nasim Sanati
    Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, 97239, USA.
  • Liam Beckman
    Oregon Health and Science University, Portland, OR 97239, USA.
  • Xiang Shao
    Oregon Health and Science University, Portland, OR 97239, USA.
  • Antonio Fabregat
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
  • Konstantinos Sidiropoulos
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
  • Julieth Murillo
    Centro Internacional de Entrenamiento e Investigaciones Médicas, Cali 18 # 122-135, Colombia.
  • Guilherme Viteri
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
  • Justin Cook
    Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
  • Solomon Shorser
    Ontario Institute for Cancer Research, Toronto, ON, M5G 0A3, Canada.
  • Gary Bader
    The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.
  • Emek Demir
    School of Medicine, Oregon Health & Science University, Portland, OR, USA.
  • Chris Sander
    Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, 10065 NY; and arne@bioinfo.se debbie@hms.harvard.edu cccsander@gmail.com.
  • Robin Haw
    Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
  • Guanming Wu
    Oregon Health Sciences University, Portland, OR, United States.
  • Lincoln Stein
    Informatics and Bio-computing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
  • Henning Hermjakob
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Peter D'Eustachio
    Department of Biochemistry & Molecular Pharmacology, NYU. Langone Medical Center, New York, NY, United States.

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