CGD Help: Searching Phenotype Data

Contents

• Searching and Browsing Phenotype Data
• Downloading and Analyzing Search Results

Searching and Browsing 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 gene.

• 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:
  • 10 Phenotypes [Expanded Phenotype Search]

  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.

• Phenotype 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 with them.

• 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.

Downloading and Analyzing Search Results

• 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.
  • GO 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.

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