Abstract
FlyAtlas 2 (www.flyatlas2.org) is part successor, part complement to the FlyAtlas database and web application for studying the expression of the genes of Drosophila melanogaster in different tissues of adults and larvae. Although generated in the same lab with the same fly line raised on the same diet as FlyAtlas, the FlyAtlas2 resource employs a completely new set of expression data based on RNA-Seq, rather than microarray analysis, and so it allows the user to obtain information for the expression of different transcripts of a gene. Furthermore, the data for somatic tissues are now available for both male and female adult flies, allowing studies of sexual dimorphism. Gene coverage has been extended by the inclusion of microRNAs and many of the RNA genes included in Release 6 of the Drosophila reference genome. The web interface has been modified to accommodate the extra data, but at the same time has been adapted for viewing on small mobile devices. Users also have access to the RNA-Seq reads displayed alongside the annotated Drosophila genome in the (external) UCSC browser, and are able to link out to the previous FlyAtlas resource to compare the data obtained by RNA-Seq with that obtained using microarrays.
Highlights
For almost ten years the FlyAtlas database [1] and web application [2] has provided research workers with information regarding the expression of genes in the tissues of Drosophila melanogaster, one of the most important model eukaryotic organisms
Despite the great utility of the FlyAtlas resource, the technology on which it is based––hybridization to Affymetrix microarrays [4]––has limitations: most notably that it does not differentiate between the extent of expression of different mRNA transcripts for the same gene, and that the probe sets are frozen in time, based on the original (2000) release of the Drosophila genome
The most important changes in the FlyAtlas 2 database are the inclusion of data for the expression of individual transcripts, for the expression of microRNAs, and of separate data for male and female flies in adult somatic tissues
Summary
For almost ten years the FlyAtlas database [1] and web application [2] (hereafter referred to as ‘FlyAtlas 1’) has provided research workers with information regarding the expression of genes in the tissues of Drosophila melanogaster, one of the most important model eukaryotic organisms. Despite the great utility of the FlyAtlas resource, the technology on which it is based––hybridization to Affymetrix microarrays [4]––has limitations: most notably that it does not differentiate between the extent of expression of different mRNA transcripts for the same gene, and that the probe sets are frozen in time, based on the original (2000) release of the Drosophila genome. In addition to providing information on gene transcripts, the RNA-Seq approach has eliminated the previous ambiguity for genes for which the microarray probe sets turned out not to be unique [2], and has produced data with the capacity to be reprocessed to accommodate future revisions of the Drosophila reference genome
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