Phenotypes

To make phenotype annotations, you need to add genotypes first: see how to add genotypes

Video summary

Making an annotation

On the Quick Links list, click on Phenotype to open a window that requires you to indicate:

• Genotype: you can choose from the genotypes added to the session from a dropdown (see how to add genotypes). Click on the magnifying glass on the right to use a search box instead of a drop-down menu.
• Term name: a FYPO term describing the phenotype associated with the genotype you selected above.
  • Start typing a phenotype in the search box. If you do not find the precise phenotype you are looking for, choose a broad term (e.g. abnormal spindle) that can be refined later.
  • Click the chosen term, and verify that the displayed definition describes the phenotype you want to annotate. There is sometimes a "Comment" section with extra tips for annotation.
  • If the blue button reads Next, click it and see if you can find a more specific term that the one you originally selected. If so, select it and do as before.
  • Otherwise, click Finish.
  • If you do not find the term you require, select a broader term, and request a new one clicking on Suggest a new term on the right side of the text box.

• Annotation extension: this field appears once you have selected a phenotype term. Always click the Add button to see if you can specify:

  • Penetrance: proportion of cells in the population that show the phenotype, can be a qualitative value or a percentage.
  • Severity: qualitative value to capture the strength of the phenotype. This is specially useful when several mutants show the same phenotype with different strength (e.g. cells being elongated).

  • Others: certain terms allow for other extensions. In general they are self-explaining, but here some important clarifications:

    Other extensions

    • Localisation phenotypes: assayed protein or transcript extensions should be used to indicate the affected gene product. If a mutation in gene X affects its localisation, choose X in assayed protein. If it affects the localisation of protein Y, choose Y. If it affects both, make one annotation for each.
    • Catalytic activity phenotypes: similarly, if a mutation in enzyme X affects its activity, still specify gene X in assayed enzyme, and if X auto-phosphorylates, indicate it in assayed substrate. A mutation in gene X may also affect catalytic activity of Y, then use Y in assayed enzyme
    • Interaction phenotypes: Indicate always two gene products. Mutation in gene X may affect interaction of proteins Z and Y, or of protein X with Y. If a mutation affects a protein/RNA interaction with itself, add the same protein twice.
    • Assayed region extension: depending on the phenotype, you will be able to select from either:
      • Genes: e.g. to indicate that a mutation gene X causes "abnormal chromatin organization" in the region of gene Y, you select assayed region or gene with gene Y. If several genes are affected, create multiple annotations.
      • Sequence ontology term: to indicate that the phenotype affects a type of sequence (e.g. centromeric repeat).

• Evidence code: the type of experiment where the phenotype was observed.

• Conditions: Conditions are aspects of the experimental setup that are independent of what cells, strain, organism, etc. are used. Type and select from the autocomplete options. Several conditions can be added, and capture the medium or temperature used, presence of chemicals, agar plates or liquid culture, etc.
• Comment: it's very useful for us if you indicate the figure or table where this phenotype comes from.

These are just the basics, more info and edge cases can be found in the FAQs