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.

modENCODE RNA-Seq temporal expression coverage data for each developmental stage were intersected with FlyBase exons (D. melanogaster Annotation Release 5.26) to calculate a single value reflecting average coverage per kb per gene. Each gene data point was then classified into one of nine expression level bins, and the graphical and text summaries were produced from the binned values.

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. These values were distributed into five expression level bins for further analysis.