FB2016_03, released May 24, 2016

A Database of Drosophila Genes & Genomes

Improvements to Expression Pattern Data

FlyBase is pleased to announce an "Expression Patterns" search in QueryBuilder, a new feature to allow for robust searching of gene expression data. This new search interface makes it possible to search for gene expression patterns by developmental stage, body part, and subcellular location. The new interface can be accessed by choosing "Expression Patterns" from the DataSet pull-down menu.

We have also improved the organization and display of expression pattern data. Major changes and enhancements include:

All gene and reporter expression patterns now use valid controlled vocabulary terms, so that every term is linked to its TermLink report. Expression pattern statements are now grouped by the assay used to experimentally determine the gene expression pattern.

Expression pattern statements are now sorted by developmental stage, rather than alphabetically, making it easier to use the collection of statements to understand dynamic developmental changes in gene expression.

Searches exploit the hierarchical organization of the Controlled Vocabulary . For example, if an expression pattern statement specifies that a gene is expressed in the embryonic brain at embryonic stage 12, a search for genes expressed in the embryonic central nervous system during the embryonic stage will include that gene among the results. The expression patterns of transgene insertion and transgenic construct reporters are not yet searchable with this tool, but will be in a future update.

Additional features we would like to draw your attention to include:

Many useful tissue-specific markers have been recorded, and can be found in the "Marker For" field on the Gene, Gene Expression, Recombinant Construct, and Insertion Reports. These can be searched using QueryBuilder.

Gene Reports display only a summary of gene expression data. The FlyBase Gene Expression Report, to which there is a link on each Gene Report page, has more extensive information. This includes free-text commentary describing expression patterns, and a list of all references for which expression data for the gene has been curated.