Gene Level High Throughput Expression Data
As a complement to our presentation of RNA-Seq and FlyAtlas expression data on our GBrowse genome browser, FlyBase now provides a gene level summary view of these data within the FlyBase Gene Reports and the ability to query on these data for particular temporal or tissue expression patterns.
In a departure from our previous policy of not presenting new data types until they are fully integrated into the FlyBase web layouts, in order to roll these data out more quickly, we are presenting beta versions in pdf format. This also gives us the opportunity to get feedback from our users on your preferences for presenting these very important data sets, through a brief survey. You can access the survey from here, or from a link in the new subsection in the corresponding gene report ( Expression Data → High-Throughput Expression Data ). We ask you to fill out this survey after you've had an opportunity to explore these data.
Computing Expression Levels: In order to summarize these data at the gene level, it was necessary first to determine a single value for the expression level of each gene at each developmental stage or tissue. For modENCODE RNA-Seq coverage data, which are continuous across the genome, we determined the normalized mean level of coverage for the exonic regions of each gene that did not overlap other neighboring genes. For the FlyAtlas larval and adult tissue data, FlyAtlas provided mean coverage levels for Affy2 probe sets, and FlyBase intersected these probe sets with the exons of all FlyBase genes to associate each probe set with one or more FlyBase genes.
Accessing High Throughput Gene Expression Summaries: The summary page for each D. melanogaster gene is located on the respective gene report in the “Expression Data” section. A thumbnail is located in the subsection called “High throughput expression data”. Clicking the thumbnail will allow you to view the full summary report in pdf format. A direct link to the full summary report can also be found in any Gene Hit List via the hyperlink labeled “Expr”. Alternatively, the summaries can be accessed directly through our QuickSearch tool by selecting the “expression summary (high throughput)” data class and typing a gene symbol.