Gene Ontology, SARS-CoV-2 and COVID-19

SARS-CoV-2 - Coronavirus

In an effort to assist global research on the SARS-CoV-2 virus (the cause of the COVID-19 disease), the Gene Ontology Consortium has made a central point of access to the relevant information available in our knowledgebase. Currently, we have compiled the following information:

  • functions of human proteins used by the virus to enter a human cell
  • functions of human proteins possibly targeted by the virus after cell entry
  • The Gene Ontology is a knowledgebase of descriptions of gene function that are both human-readable and computer-readable, based on evidence in the scientific literature. Because the GO knowledgebase is readable by computers, it enables computational analyses of biological systems and experimental results, accelerating biomedical research. Read more.

    The “GO Ribbon” viewer below displays a horizontal list of broad categories of functions that a gene (or a protein encoded by a gene) can have. A colored box under that category indicates that the gene is known to have a function of that type, while a blank box indicates a function it is not known to have. Clicking on a colored box will bring up another page with more details, such as a more precise description of the function, and links to additional information such as the scientific evidence it is based on, and the specific GOC group that curated the information.

    You can also download this information for use in computational analyses:

  • GO annotations for the human genes that may be relevant for SARS-CoV-2 infection3: [GAF] [GPAD] [GPI]
  • Human genes that may be relevant for SARS-CoV-2 infection3: [Excel table] [JSON]
  • GO annotations for the SARS-CoV-2 virus genes: [GPAD] [GPI]
  • the full GO knowledgebase
  • Learn more about: [GAF] [GPAD] [GPI].

    Human proteins used by SARS-CoV-2 to enter human cells

    The virus has been shown to require two human proteins (ACE2, TMPRSS2) for cell entry1,2. These are the same proteins used by SARS-CoV4, the cause of the 2002-2004 SARS epidemic.
    Ribbon Tips:
  • click on the gene name of a ribbon line to show all GO terms (functions/processes/locations) associated
  • click on a high-level diagonal GO term (e.g. signaling) to show the term details and associated genes
  • click on a ribbon cell to show the detailed annotations for the selected high-level GO term
  • Other human proteins that are possible targets of SARS-CoV-2

    The SARS-CoV-2 viral genome encodes instructions for making 29 different proteins5. A recent study by Gordon et al.3 expressed and purified 27 of those proteins, and tested them to see which human proteins they physically interact with. They found specific human protein interactions for 26 SARS-CoV-2 proteins. These human proteins may be targets of the SARS-CoV-2 virus, and enable the virus to infect human cells, replicate, and spread.

    Select one of the SARS-CoV-2 proteins to see the list of human proteins it interacts with3, and the normal functions of those human proteins. Scanning vertically down a column can help to see the functions these human proteins have in common, and may indicate how the virus may be using or disrupting normal human cell functions during infection.

    SARS-CoV-2 gene:
    Ribbon Tips:
  • click on the gene name of a ribbon line to show all GO terms (functions/processes/locations) associated
  • click on a high-level diagonal GO term (e.g. signaling) to show the term details and associated genes
  • click on a ribbon cell to show the detailed annotations for the selected high-level GO term
  • LIVE GO ENRICHMENT ANALYSIS (?)
    GO enrichment detects processes, functions or components that are unusually represented in a gene set. For the above human proteins that interact with , find (if any) the unusually represented :

    GO enrichment analysis of human proteins targeted by SARS-CoV-2

    Click one of the following button to perform a live GO enrichment analysis of human proteins that physically interact with SARS-CoV-2 proteins. This analysis shows the human biological functions that may be preferentially targeted by the SARS-CoV-2 virus.

    Ongoing work of the GO Consortium

    • Integrating the SARS-CoV-2 genes to allow for the curation and reuse of recent articles on SARS-CoV-2.
    • Producing GO-CAMs to further detail the infectious mechanisms of SARS-CoV-2.
    • Providing interactive jupyter notebooks to learn how to rapidly use and integrate GO data in larger analysis.

    References