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CGD Help: Searching Phenotype Data
The organization of mutant phenotype data in CGD is described in the
Phenotype Pages Help document. The
data 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
- CGD Quick Search. Any text entered into the Quick
Search box is used to
search the list of phenotype
terms describing observed features, as well as other kinds of data
in CGD. When a query is entered into the search box, the results
page lists the matches found in various types of data. A typical
Phenotype result would appear as:
The phrase "10 Phenotypes" is hyperlinked to a list
of phenotypes for which the search criterion
matches all or part of a phenotype term. The "Expanded Phenotype
Search" link is hyperlinked to a list of search results in which the
original search criterion has been used to search all phenotype data,
including the terms describing observable features and other
associated information such as details, conditions, chemical names,
and virulence models.
- Expanded Phenotype
Search. This interface allowing a complete search of phenotype data may be accessed
directly from the Search Options
page. Note that gene names, systematic names, and aliases are not
included in this search, although
gene names may be found within phenotype data where they are part of
allele or Reporter names.
Terms page. This page allows you to view the entire hierarchical list of phenotype
terms that are in use at CGD. Clicking on any term on this page leads to a list of
all phenotypes annotated using this term, and the genes associated
- Tables displaying phenotype data. Phenotype terms and
chemical names that occur within any tables of phenotype data (e.g.,
on the Phenotype Details page showing mutant
phenotypes for a single gene, as well as in tables of 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.
Go to the Expanded Phenotype
- The Analyze Gene List link at the top of every phenotype
search results page leads to a box at the bottom of the page
containing several links that allow you to further analyze or to
download the list of genes displayed.
Term Finder: leads to the GO Term Finder interface pre-filled
with the list of genes. GO Term Finder finds
Gene Ontology (GO) terms that the genes have in common, revealing
shared biological processes, functions, or subcellular locations of
the gene products. A detailed description of the GO Term Finder tool
is available on its help page.
GO Slim Mapper: leads to the
GO Slim Mapper interface, pre-filled with the list of genes. GO Slim
Mapper maps specific GO terms to broader parent terms (GO
Slim terms), giving an overview of the processes, functions, or
cellular components to which genes in a list are annotated. More
information about the GO Slim Mapper tool is available on its help page.
- View GO Annotation Summary: leads to a summary of
the GO annotations for the genes in the list. The list is divided into
three tables, each containing terms from one aspect of GO (biological
process, molecular function, cellular component) and showing how many
of the genes in the list are annotated to each term.
- Download Data: allows you to download all of the
search results, including the list of genes and the associated
phenotype data, as a tab-delimited file.
- Download options: leads to the Batch
Download interface, pre-filled with the list of genes. This
interface allows you to download various types of information for the
genes in a list, including DNA and protein sequence, chromosomal
feature information, GO annotations, phenotype annotations, and
S. cerevisiae orthologs and best hits.
- In addition, files containing phenotype data for all genes in each species are available for download from CGD's Download Data page.