Gene Page: Phenotypes

PomBase defines a phenotype as an observable characteristic, or set of characteristics, of an organism that results from the interaction of its genotype with a given environment. In PomBase, phenotypes are annotated using terms from the Fission Yeast Phenotype Ontology (FYPO). FYPO uses several existing ontologies from the Open Biological and Biomedical Ontologies (OBO) collection to construct formal definitions. Basic documentation for FYPO is available at the OBO Foundry, and further information is available on the PomBase wiki.

In the phenotype annotation display on PomBase gene pages, the first item shown is a brief summary indicating whether cells with a null (deletion) allele of the gene are viable or inviable, or either depending on experimental conditions. Next, single-allele phenotypes are shown in two tables. The first table lists phenotypes observed at the population level, such as viability in culture, and the second shows cell-level phenotypes. Note that the viable/inviable population terms describe whether a gene is essential or not, and see the wiki FYPO Content and Structure documentation for more information on cell and population phenotypes. Finally, two more tables list population-level and cell-level multi-allele phenotypes, i.e. phenotypes associated with double mutants, triple mutants, etc, and the relevant genotype details.

Each table includes ontology term details and supporting data. The Summary view shows just the essentials; each unique combination of gene, FYPO term, allele(s) and extension(s) is shown once. For single-allele phenotypes, the display includes:

gene page phenotype annotations

  1. The FYPO term name, which links to a page with additional information, including the term definition, any synonyms, relationships to other FYPO terms, and a list of genes annotated to the term.
  2. Allele details, including a name (if one is used in the literature) and description (where known). The column is headed "Genotypes" for consistency between the single- and multi-allele displays. Mouse over the allele name to show the allele type, which indicates whether partial deletions or altered residues refer to amino acids or nucleotides. If you can provide a description for any allele shown as "unknown", please contact the PomBase curators.
  3. Link to a page with term details and a list of genes annotated to the term and its is_a and part_of descendants (the GO documentation on Ontology Structure and Ontology Relations has some useful information on this topic).
  4. Phenotype annotations may have extensions to capture expressivity (the extent to which a phenotype is expressed; for PomBase annotations expressivity extensions are often used to capture information about phenotype severity) or penetrance (proportion of a population that shows the phenotype), or to document which gene or protein used in an assay for level, localisation, etc. S. pombe genes link to PomBase gene pages. Expressivity and penetrance use the relations has_expressivity and has_penetrance respectively, and can have values such as "high", "medium", or "low" (numerical values may be added in the future if and when the need arises). A gene or gene product used in an assay is stored using the appropriate PomBase systematic ID and the relation assayed_using; the relation is converted to affecting in the gene page display. If a mutation affects an activity that modifies another gene product, extensions may capture the affected enzyme, the affected substrate, or both. The relation assayed_enzyme is displayed as affecting activity of on gene pages, and assayed_substrate is shown as affecting substrate.

The Full single-allele phenotype view shows more details, including separate entries for repeat determinations of a given gene/term/allele/extension combination (if supported by more than one line of evidence and/or reported in more than one paper):

gene page phenotype annotations

  1. The unique ID and name for a term in the phenotype ontology. The ID links to a page with additional information, including the term definition, any synonyms, relationships to other FYPO terms, and a list of genes annotated to the term.
  2. A brief descriptor for the type of evidence that supports the annotation. The evidence categories come from the Evidence Ontology (ECO). The evidence text may be nested under the term name to save space.
  3. Allele details, including a name (if one is used in the literature) and description (where known). Mouse over the allele name to show the allele type, which indicates whether partial deletions or altered residues refer to amino acids or nucleotides. If you can provide a description for any allele shown as "unknown", please contact the PomBase curators.
  4. Where available, the expression level of the allele in the experiment is shown here. Both allele and expression details are subheadings under "Genotype", again for consistency.
  5. Information about experimental conditions, such as temperature, type of medium used, etc. Descriptions come from a small ontology maintained by PomBase curators.
  6. The paper from which the annotation comes.
  7. Link to a page with term details and a list of genes annotated to the term and its is_a and part_of descendants (the GO documentation on Ontology Structure and Ontology Relations has some useful information on this topic).
  8. Phenotype annotations may have extensions to capture expressivity (the extent to which a phenotype is expressed; for PomBase annotations expressivity extensions are often used to capture information about phenotype severity) or penetrance (proportion of a population that shows the phenotype), or to document which gene or protein used in an assay for level, localisation, etc. S. pombe genes link to PomBase gene pages. Expressivity and penetrance use the relations has_expressivity and has_penetrance respectively, and can have values such as "high", "medium", or "low" (numerical values may be added in the future if and when the need arises). A gene or gene product used in an assay is stored using the appropriate PomBase systematic ID and the relation assayed_using; the relation is converted to affecting in the gene page display. If a mutation affects an activity that modifies another gene product, extensions may capture the affected enzyme, the affected substrate, or both. The relation assayed_enzyme is displayed as affecting activity of on gene pages, and assayed_substrate is shown as affecting substrate.

Similar displays are used for multi-allele phenotypes. The "Count" column is omitted to avoid complications arising from having more than one gene connected with almost every multi-allele phenotype.

The multi-allele Summary shows FYPO terms and genotype descriptions:

multi-allele FYPO summary view on gene page

  1. The FYPO term name, which links to a page with additional information, including the term definition, any synonyms, relationships to other FYPO terms, and a list of genes annotated to the term.
  2. Genotype details, including a name (if one is used in the literature) and descriptions for the relevant alleles (where known). Mouse over any allele name to show the allele type.

The Full view includes more details:

multi-allele FYPO full view on gene page

  1. The unique ID and name for a term in the phenotype ontology. The ID links to a page with additional information, including the term definition, any synonyms, relationships to other FYPO terms, and a list of genes annotated to the term.
  2. A brief descriptor for the type of evidence that supports the annotation. The evidence categories come from the Evidence Ontology (ECO). The evidence text may be nested under the term name to save space.
  3. Each gene included in the genotype description is listed on one line per allele present (some genotypes include two or more different alleles of the same gene), and linked to its gene page.
  4. Allele descriptions are shown essentially as in the single-allele display, including the mouse-over that shows the allele type.
  5. Where available, the expression level of the allele in cells with the genotype is shown here. Gene, allele and expression details are subheadings under "Genotype".
  6. Information about experimental conditions, such as temperature, type of medium used, etc.
  7. The paper from which the annotation comes.

Annotation extensions are also included in the multi-allele Summary and Full views (although none are included for the annotations in the above illustrations), using the same display as for single-allele phenotypes.

Also see the Advanced Search documentation for information on finding genes annotated to phenotype terms.