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Protein modification

To create a protein modification annotation, on the Quick Links list, click on Protein modification to open a window that requires you to indicate:

  • Gene: gene of which the protein is modified. See how to add genes
  • Term name: a term from the MOD ontology to represent the modification. Some can be tricky to find, see below.
  • Annotation extensions: available once a term is selected. Most are self-explaining, but some clarifications:
    • Extensions that contain during, allow you to specify:
      • A cell cycle phase (e.g. removed during anaphase)
      • A cellular response to a stress (e.g. present during cellular response to heat)
    • Extensions that contain in presence of allow to add a chemical, drug or metabolite (e.g. galactose or hydroxyurea).
    • Extension in absence of allows you to indicate that the modification is exist when a certain gene is missing (e.g. deletion of gene X leads to the phosphorylation of protein Y).
    • For proteins that modify themselves, use added by with the same gene as the Gene field of the modification.
    • You can use position modified to indicate the affected residue or residues (comma-separated).
  • Evidence code: can only be Inferred from Direct Assay.
  • Comment: it's very useful for us if you indicate the figure or table where this interaction comes from.

Modifications that are tricky to find

  • Phosphorylation: below the term names and their MOD codes, which can be used in the Term name field.
    • Serine: O-phospho-L-serine (MOD:00046)
    • Threonine: O-phospho-L-threonine (MOD:00047)
    • Tyrosine: O4'-phospho-L-tyrosine (MOD:00048)
  • Methylation: there are many terms, we recommend starting from "methylated residue" (MOD:00427), and iterate towards more specific terms.
  • Glycosilation: there are more specific terms, but "N-glycosylated residue" (MOD:00006) or "O-glycosylated residue" (MOD:00396) are often sufficient.