CGD Help: Phenotype Pages

Contents

Description
Mutant phenotype data
Navigating mutant phenotype data
Other Relevant Links
Associated Glossary Terms

Description

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, 'phenotype_data.tab', 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.

Experiment type indicates the method used to detect and analyze mutant phenotypes. The major experiment types are classical genetics and large-scale survey. These indicate the scope of the experiment and the methods used. Experiments of the type classical genetics are small-scale, focusing on one or a few genes. Large-scale survey experiments are those designed with a knowledge of the genome sequence, often using high-throughput, robot-assisted techniques.
Classical genetics experiments are further categorized into three sub-types to indicate the ploidy of the strain in which the phenotype was analyzed: aneuploid, homozygous diploid, and heterozygous diploid. Note that in cases of aneuploidy, the experiment type refers to the ploidy of the mutant allele: if it is carried on a triploid region of the genome, the "aneuploid, classical genetics" experiment type will be used, but if it is carried on a diploid region of the genome, the "homozygous diploid, classical genetics" or "heterozygous diploid, classical genetics" experiment types will be used. For haploid Candida species, such as C. glabrata, "haploid, classical genetics" is used to indicate its ploidy.

Large-scale survey experiments are further categorized into sub-types reflecting the ploidy of the strain used and also the experimental methodology:
- systematic mutation set refers to the use of genome-wide mutant collections.
- competitive growth refers to experiments in which pools of mutant strains are grown together for many generations to assess their relative fitness.
Mutant information includes a description of the impact of the mutation on the activity of the gene product. Mutations are classified into the following types:
- activation - the mutation increases the normal activity of a gene product
- conditional - the activity of the gene product appears wild-type under some conditions and altered under others
- dominant negative - the mutant gene product negatively affects the activity of the wild-type gene product, often by dimerizing with it or titrating one of its targets
- gain of function - the mutation confers a new activity on the gene product
- misexpression - the gene product is expressed at a developmental stage, in a cell type, or at a subcellular location different from that at which the wild-type gene is expressed
- null - synonymous with "loss of function", this type of mutation abolishes the function of a gene product. Point mutations as well as complete deletions may result in a null phenotype.
- overexpression - the gene is expressed under control of a strong promoter and/or on a high copy number plasmid so that the gene product is present at higher levels than wild-type
- reduction of function - the mutation reduces the activity of the gene product
- repressible - synonymous with depletion, this represents cases where there is a reduction of levels of the gene product, often through the use of a repressible promoter, and may often be combined with an N-degron to stimulate rapid gene product turnover.
- unspecified - used when the mutant type cannot be determined
Allele names and descriptions, where recorded, are also displayed in this column of the table. Note that if an allele was named using an alternative gene name, we have combined it with the CGD standard gene name: for example, the HGT4-1 allele of the SNF3 gene is noted as SNF3-(HGT4-1). We make an effort to capture as much allele information as possible, but are unable to comprehensively record all alleles.
Strain background captures the genetic background in which the mutant phenotype was analyzed, for some of the most commonly used strains. The strain backgrounds that are recorded at present are:
C. albicans:
- BWP17
- CAF2-1
- CAI-4
- CAI-8
- P37005
- RM1000
- SC5314
- SN152
- SN87
- SN95
- WO-1
- Other
- Not recorded
C. glabrata:
- 2001HT
- 2001T
- BG14
- BG2
- CBS138 (ATCC2001)
- NCCLS84
- Other C. glabrata
If a study uses a strain backgound that is isogenic to one on this list, then the parent background is captured. If a background is used that is not traceable to a strain on this list, or not stated in the paper, it is noted as 'Other'. Strain background is listed as 'Not recorded' for some mutant phenotypes that were curated before we began capturing this information.
Phenotype combines a term describing the observed feature with a qualifier that indicates the direction of the change in that feature relative to wild type (abnormal, arrested, decreased, decreased duration, decreased rate, delayed, absent, increased, increased duration, increased rate, premature, normal, normal duration, normal rate). The entire list of terms describing observed features, which are arranged in a hierarchical fashion, is displayed on a page on which each term is linked to the list of phenotypes annotated using that term.
In creating the terms that describe phenotypes, we have tried to strike a balance between using concise, descriptive vocabulary while also including well-known, commonly used expressions such as "auxotrophy". These "classical" phenotypes are not used in combination with a qualifying term (e.g., "increased"), since the direction of change relative to wild type is already implicit. In order to describe phenotypes involving resistance or sensitivity to drugs, chemicals, or conditions, we use "resistance" by convention; thus "sensitivity" is described as "decreased resistance". The exceptions to this are temperature and pheromone sensitivity, which are so commonly referred to as sensitivity that we have created individual terms for these concepts. Note that the phenotypes viable and inviable refer to viability under standard growth conditions.
The controlled-vocabulary terms used to describe phenotypes are a subset of the terms in the Ascomycete Phenotype Ontology (APO).
Anatomical structure indicates any anatomical structure that is affected by the mutation. Structures are described using terms from the Fungal Anatomy Ontology (FAO).
Chemical indicates any chemical compounds used in the phenotype assay, most commonly exogenous chemicals that affect the growth of the mutant strain, but also including nutrient sources, enzymatic substrates, etc. Chemical compound names are derived, where possible, from the Chemical Entities of Biological Interest (ChEBI) database maintained at the European Bioinformatics Institute.
Details includes additional types of information about the phenotype, captured as free text:
- Condition summarizes relevant experimental conditions such as growth media or temperature
- Details includes any additional facts that are important to understanding the phenotype
- Reporter identifies the protein(s) or RNA(s) that are used in an experiment to track a process such as transport or localization of gene products
Virulence model indicates the type of model system used to assess the virulence of a mutant. The model systems that are currently captured are:
- C. elegans infection
- ex vivo model of infection
- guinea pig intravenous infection
- immunosuppressed mouse intravenous infection
- in vitro model of infection
- insect infection
- mouse corneal infection
- mouse cutaneous infection
- mouse gastrointestinal tract infection
- mouse intravenous infection
- mouse mammary gland infection
- mouse oropharyngeal infection
- mouse peritoneal infection
- mouse pulmonary infection
- mouse vaginal infection
- other model
- rabbit corneal infection
- rat oropharyngeal infection
- rat peritoneal infection
- rat vaginal infection
References lists the publication(s) in which the phenotype is described, with links to their "CGD Curated Paper" pages as well as to their abstracts in PubMed.

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.

Associated SGD Glossary Terms


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