SGD Help: Phenotypes

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.

All of the phenotype data for a particular gene may be downloaded to your computer, as a tab-delimited text file, via the 'Download' button below the Annotations table. A file containing phenotype data for all genes, 'phenotype_data.tab', is available for download.

SGD's mutant phenotype curation system is described in Costanzo MC, et al. (2009) New mutant phenotype data curation system in the Saccharomyces Genome Database. Database (Oxford) 2009:bap001 PMID: 20157474.

Contents

  1. Mutant phenotype data
    1. What is a mutant phenotype?
    2. How phenotype data are recorded in SGD
  2. The Phenotype page
    1. Phenotype Overview
    2. Annotations
    3. Shared Phenotypes
    4. Resources
  3. Searching and browsing mutant phenotype data

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 SGD, our working definition of a phenotype is the effect of a mutation on any observable or detectable feature of yeast cells, colonies, or cultures. We limit our curation to those features that are observable in living cells or that occur in living cells (though 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 SGD as Gene Ontology (GO) annotations.

The SGD Phenotype pages display only single mutant phenotypes. Phenotypes resulting from genetic interactions are shown on the Interactions pages, which are accessible from the Interactions tab of the Locus Summary or from a link in the Interactions section of the Locus Summary.

How phenotype data are recorded in SGD

In order to facilitate searching and comparison of related phenotypes, SGD has 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: Phenotype, Experiment type, Mutant information, Strain background,  Chemical, Details, and Reference.

  • 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 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', 'sterile', and 'petite'. 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 for S. cerevisiae: glucose-containing rich medium (YPD) at 30 deg C under aerobic conditions.

  • 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. They are further categorized into two sub-types:

    • systematic mutation set refers to the use of genome-wide mutant collections such as the set of systematic deletion strains.
    • competitive growth refers to experiments in which pools of mutant strains are grown together for many generations to assess their relative fitness.

    For all experiment types, haploidy is implicit unless otherwise stated. If homozygous or heterozygous diploid strains were used in an experiment, the experiment type indicates this.

  • 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 mutation increases the normal activity of a gene product
    conditional activity of the gene product appears wild-type under some conditions and altered under others
    dominant negative 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 mutation confers a new activity on the gene product
    misexpression 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 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 mutation reduces the activity of the gene product
    repressible synonymous with depletion, represents cases in which the level of the gene product is reduced, often through the use of a repressible promoter (for example, the tet promoter in the presence of tetracycline, or the GAL1 promoter in the presence of glucose); 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 SGD Standard gene name: for example, the whi1-310 allele of the CLN3 gene is noted as cln3-(whi1-310). 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:

    CEN.PK, D273-10B, FL100, JK9-3d, RM11-1a, S288C, SEY6210, SK1, Sigma1278b, W303, X2180-1A, and Y55.

    See the SGD Wiki for information about and references for these strains. If a study uses a strain background 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 not displayed for some mutant phenotypes that were recorded before we began capturing this information.

  • 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.
  • Reference shows the publication from which a phenotype was curated, with a link to its "Reference" page in SGD.

The Phenotype page

Context-Specific Information and Help

Please note that context-specific information and help can be found on the Phenotype page itself, connected directly with specific data sections on that page. Just click on the information icon to pop-up short descriptions of the data or the help icon for help in using the table, graph, or visualization displaying the data.

Phenotype Overview

The Phenotype Overview summarizes phenotype curation for a particular gene. The graph on the left shows the number of annotations for that gene involving different mutant types, separated into classical genetics and large-scale studies. The graph on the right shows the number of annotations for that gene involving different S. cerevisiae strain backgrounds.

Annotations

The Annotations table contains the following columns: Phenotype, Experiment type, Mutant information, Strain background,  Chemical, Details, and Reference. See above for descriptions of each column. At the upper right of the table, the "Filter" box allows you to type any text in order to display in the table only the rows containing that text. Each column header contains up and down arrows that allow you to sort the table by that column in ascending or descending order. At the bottom of the table, you can choose how many records to display in the table, or choose which pages of the table to view. The Download link at the bottom of the table allows you to download its entire contents as a text file. If you have filtered the table, the Download link creates a file containing only the rows that meet your filtering criteria.

Shared Phenotypes

This network diagram allows you to visualize connections between different genes, in the form of phenotypes they share. The diagram displays phenotype observables (purple squares) that are shared between the given gene (yellow circle) and other genes (gray circles) based on the number of phenotype observables shared (adjustable using the slider at the bottom).

Click on a gene or phenotype observable name to go to its specific page within SGD; drag any of the gene or observable objects around within the visualization for easier viewing; click “Reset” to automatically redraw the diagram; filter the genes that share observable terms with the given gene by the number of terms they share by clicking anywhere on the slider bar or dragging the tab to the desired filter number.

The network diagram may be downloaded as a .png image by using the Download link underneath the graphic.

Resources

At the bottom of the Phenotype page is a list of additional resources, external to SGD, that are relevant for S. cerevisiae mutant strain and phenotype information. Where possible, links lead to information in other databases about the specific gene of the page.

Searching and Browsing Phenotype Data

The phenotype data in SGD may be browsed and searched via several avenues:

  • Locus Summary: Locus-specific lists of single mutant phenotypes are displayed on the Locus Summary page for each gene or feature; the Phenotype tab leads to a table containing all mutant phenotypes curated for that gene.
  • SGD Search: Any text entered into the Search box at the top of most SGD pages will be used to search all phenotype data. When a query is entered into the search box, the results page lists the matches found in various types of data. The "Phenotypes" link leads to a table showing the phenotype search results in detail.
  • Phenotype Terms page. This page allows you to view the entire hierarchical list of phenotype terms. Clicking on any term on this page leads to a list of all phenotypes annotated using this term, and the genes associated with them.
  • Tables displaying phenotype data: Phenotype terms and chemical names that occur within any tables of phenotype data (mutant phenotypes for a single gene; phenotype search results) provide access to additional related phenotypes and the genes associated with them. Clicking on a hyperlinked 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.
  • YeastMine allows retrieval of chromosomal features using multiple criteria, including phenotype observables and other custom queries.
  • SGD Downloads Site: A file containing phenotype data for all genes, 'phenotype_data.tab', is available for download.