Using Reactome to build an autophagy mechanism knowledgebase

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

Research output: Contribution to journalArticlepeer-review

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. Abbreviations: CMA: chaperone-mediated autophagy; GO: Gene Ontology; MA: macroautophagy; MI: microautophagy; MTOR: mechanistic target of rapamycin kinase; SQSTM1: sequestosome 1.

Original languageEnglish (US)
Pages (from-to)1543-1554
Number of pages12
JournalAutophagy
Volume17
Issue number6
DOIs
StatePublished - 2021

Keywords

  • Annotation
  • Reactome
  • autophagy
  • biocuration
  • curation
  • enrichment analysis
  • knowledgebase
  • mechanistic analysis
  • molecular reactions
  • pathways

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

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