CGD Help: Phenotype Pages



The Phenotype page presents detailed information about single mutant phenotypes for a particular gene, along with references for each observation. This page is accessible from the 'Phenotype' tab of the Locus Summary and is also linked from the Mutant Phenotypes section of the Locus Summary, where the phenotype data are presented in summary form. Data are presented in tabular form on the Phenotype page and may continue onto additional pages if the number of phenotypes is greater than 30. All of the phenotype data for a particular gene may be downloaded to your computer, as a tab-delimited text file, through the 'Download Data' links near the top and bottom of the page. A file containing phenotype data for all genes, '', is available for download from CGD's Download Data page.

Mutant phenotype data

What is a mutant phenotype?

Broadly defined, the phenotype of a mutation is the observable effect that it has on an organism. At CGD, our working definition of a phenotype is the effect of a mutation on any observable or detectable feature of Candida cells or cultures. We limit our curation to those features that are observable in living cells or that occur in living cells (they may be detected by assays that disrupt cells). For example, an effect of a mutation in a protease-encoding gene on the processing of its substrates would be considered a mutant phenotype, even though biochemical methods must be used to detect the lack of processing. In contrast, the effect of a mutation in an enzyme on the in vitro activity of that enzyme would not be curated as a mutant phenotype. We focus on curating the primary observation rather than its interpretation: for example, we record the inability of a mutant strain to grow on medium lacking adenine, rather than the fact that it has a defect in the adenine biosynthesis pathway. Many of the more detailed, molecular effects that could be considered phenotypes, as well as the molecular interpretations of observed effects, are captured in CGD as
Gene Ontology (GO) annotations. Additionally, only single mutant phenotypes are curated at present.

How phenotype data are recorded in CGD

In order to facilitate searching and comparison of related phenotypes, we have developed a system for recording mutant phenotype data that uses a controlled vocabulary to describe most aspects of the phenotype.

Mutant phenotype data are presented in a table that contains the following columns: Experiment type, Mutant information, Strain background, Phenotype, Anatomical structure, Chemical, Details, Virulence model, and References.

Navigating mutant phenotype data

If there are more than 30 mutant phenotypes recorded for a single gene, they are separated onto multiple pages. A navigation bar above the table on each page lists the total number of phenotypes and pages, and indicates which page you are viewing. Links at the top of the page allow you to jump down to the 'Download data' link.

Within the table of phenotype data, phenotypes and chemicals are hyperlinked. Clicking on a phenotype term will take you to a list of all annotations to that phenotype, with the associated genes. Clicking on the name of a chemical will take you to a list of all phenotypes and genes associated with that chemical.

Additional options for searching phenotype data include a search of the major phenotype terms via the CGD Quick Search, which is accessed via a text entry box located at the top of most CGD pages; and a complete search of phenotypes and associated data via the Expanded Phenotype Search, which may be accessed from a link on the Search Options page as well as from the table of Quick Search results. Please see the Phenotype Search Help page for more details on searching phenotype data.

Other Relevant Links

  1. CGD Pages
    1. Search Options page
    2. Expanded Phenotype Search
    3. Phenotype Search Help page
    4. List of phenotype terms in use at CGD

  2. External Sites
    1. Open Biomedical Ontologies site: view and download the Ascomycete Phenotype Ontology and the Fungal Anatomy Ontology
    2. Home page of the Fungal Anatomy Ontology project
    3. Chemical Entities of Biological Interest (ChEBI)

Associated SGD Glossary Terms

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