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The reactome pathway knowledgebase 2022.
Gillespie, Marc; Jassal, Bijay; Stephan, Ralf; Milacic, Marija; Rothfels, Karen; Senff-Ribeiro, Andrea; Griss, Johannes; Sevilla, Cristoffer; Matthews, Lisa; Gong, Chuqiao; Deng, Chuan; Varusai, Thawfeek; Ragueneau, Eliot; Haider, Yusra; May, Bruce; Shamovsky, Veronica; Weiser, Joel; Brunson, Timothy; Sanati, Nasim; Beckman, Liam; Shao, Xiang; Fabregat, Antonio; Sidiropoulos, Konstantinos; Murillo, Julieth; Viteri, Guilherme; Cook, Justin; Shorser, Solomon; Bader, Gary; Demir, Emek; Sander, Chris; Haw, Robin; Wu, Guanming; Stein, Lincoln; Hermjakob, Henning; D'Eustachio, Peter.
  • Gillespie M; Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
  • Jassal B; College of Pharmacy and Health Sciences, St. John's University, Queens, NY11439, USA.
  • Stephan R; Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
  • Milacic M; Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
  • Rothfels K; Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
  • Senff-Ribeiro A; Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
  • Griss J; Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
  • Sevilla C; Universidade Federal do Paraná, Curitiba, 80060-000, Brazil.
  • Matthews L; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
  • Gong C; Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria.
  • Deng C; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
  • Varusai T; NYU Grossman School of Medicine, New York, NY10016, USA.
  • Ragueneau E; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
  • Haider Y; National Center for Protein Sciences Beijing, Beijing Institute of Life Omics, Beijing102206, China.
  • May B; Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China.
  • Shamovsky V; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
  • Weiser J; Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
  • Brunson T; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
  • Sanati N; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
  • Beckman L; Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
  • Shao X; NYU Grossman School of Medicine, New York, NY10016, USA.
  • Fabregat A; Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
  • Sidiropoulos K; Oregon Health and Science University, Portland, OR 97239, USA.
  • Murillo J; Oregon Health and Science University, Portland, OR 97239, USA.
  • Viteri G; Oregon Health and Science University, Portland, OR 97239, USA.
  • Cook J; Oregon Health and Science University, Portland, OR 97239, USA.
  • Shorser S; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
  • Bader G; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
  • Demir E; Centro Internacional de Entrenamiento e Investigaciones Médicas, Cali 18 # 122-135, Colombia.
  • Sander C; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
  • Haw R; Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
  • Wu G; Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
  • Stein L; The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.
  • Hermjakob H; Oregon Health and Science University, Portland, OR 97239, USA.
  • D'Eustachio P; cBio Center at Dana-Farber Cancer Institute, Boston, MA02115, USA.
Nucleic Acids Res ; 50(D1): D687-D692, 2022 01 07.
Article in English | MEDLINE | ID: covidwho-1522256
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Antiviral Agents / Proteins / Knowledge Bases Limits: Humans Language: English Journal: Nucleic Acids Res Year: 2022 Document Type: Article Affiliation country: Nar

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Antiviral Agents / Proteins / Knowledge Bases Limits: Humans Language: English Journal: Nucleic Acids Res Year: 2022 Document Type: Article Affiliation country: Nar