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Varusai TM, Jupe S, Sevilla C, et al. Using Reactome to build an autophagy mechanism knowledgebase. Autophagy. 2020;17(6):1543-1554doi: 10.1080/15548627.2020.1761659.
Varusai, T. M., Jupe, S., Sevilla, C., Matthews, L., Gillespie, M., Stein, L., Wu, G., D'Eustachio, P., Metzakopian, E., & Hermjakob, H. (2021). Using Reactome to build an autophagy mechanism knowledgebase. Autophagy, 17(6), 1543-1554. https://doi.org/10.1080/15548627.2020.1761659
Varusai, Thawfeek Mohamed, et al. "Using Reactome to build an autophagy mechanism knowledgebase." Autophagy vol. 17,6 (2021): 1543-1554. doi: https://doi.org/10.1080/15548627.2020.1761659
Varusai TM, Jupe S, Sevilla C, Matthews L, Gillespie M, Stein L, Wu G, D'Eustachio P, Metzakopian E, Hermjakob H. Using Reactome to build an autophagy mechanism knowledgebase. Autophagy. 2021 Jun;17(6):1543-1554. doi: 10.1080/15548627.2020.1761659. Epub 2020 Jun 02. PMID: 32486891; PMCID: PMC8204961.
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Autophagy. 2021 Jun;17(6):1543-1554. doi: 10.1080/15548627.2020.1761659. Epub 2020 Jun 02.

Using Reactome to build an autophagy mechanism knowledgebase.

Autophagy

Thawfeek Mohamed Varusai, Steven Jupe, Cristoffer Sevilla, Lisa Matthews, Marc Gillespie, Lincoln Stein, Guanming Wu, Peter D'Eustachio, Emmanouil Metzakopian, Henning Hermjakob

Affiliations

  1. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK.
  2. Open Targets, Wellcome Genome Campus, Cambridgeshire, UK.
  3. COSMIC, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
  4. Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY, USA.
  5. Ontario Institute for Cancer Research, Toronto, ON, Canada.
  6. Pharmaceutical Sciences, St.John's University, Queens, NY, USA.
  7. Department of Molecular Genetics, University of Toronto, Toronto, Canada.
  8. Department of Medical Informatics and Clinical Epidemiology, School of Medicine, Oregon Health and Science University, Oregon, Portland, OR, USA.
  9. UK Dementia Research Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
  10. State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for Protein Sciences, Beijing, China.

PMID: 32486891 PMCID: PMC8204961 DOI: 10.1080/15548627.2020.1761659

Abstract

The 21st century has revealed much about the fundamental cellular process of autophagy. Autophagy controls the catabolism and recycling of various cellular components both as a constitutive process and as a response to stress and foreign material invasion. There is considerable knowledge of the molecular mechanisms of autophagy, and this is still growing as new modalities emerge. There is a need to investigate autophagy mechanisms reliably, comprehensively and conveniently. Reactome is a freely available knowledgebase that consists of manually curated molecular events (reactions) organized into cellular pathways (https://reactome.org/). Pathways/reactions in Reactome are hierarchically structured, graphically presented and extensively annotated. Data analysis tools, such as pathway enrichment, expression data overlay and species comparison, are also available. For customized analysis, information can also be programmatically queried. Here, we discuss the curation and annotation of the molecular mechanisms of autophagy in Reactome. We also demonstrate the value that Reactome adds to research by reanalyzing a previously published work on genome-wide CRISPR screening of autophagy components.

Keywords: Annotation; Reactome; autophagy; biocuration; curation; enrichment analysis; knowledgebase; mechanistic analysis; molecular reactions; pathways

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