Resources for functional genomics studies in Drosophila melanogaster

Abstract

Drosophila melanogaster has become a system of choice for functional genomic studies. Many resources, including online databases and software tools, are now available to support design or identification of relevant fly stocks and reagents or analysis and mining of existing functional genomic, transcriptomic, proteomic, etc. datasets. These include large community collections of fly stocks and plasmid clones, "meta" information sites like FlyBase and FlyMine, and an increasing number of more specialized reagents, databases, and online tools. Here, we introduce key resources useful to plan large-scale functional genomics studies in Drosophila and to analyze, integrate, and mine the results of those studies in ways that facilitate identification of highest-confidence results and generation of new hypotheses. We also discuss ways in which existing resources can be used and might be improved and suggest a few areas of future development that would further support large- and small-scale studies in Drosophila and facilitate use of Drosophila information by the research community more generally.

Keywords: Drosophila: functional genomics; bioinformatics; community resources; online tools.

Figure 1

Functional genomics workflow example one. In this workflow based on J. Zirin, J. Nieuwenhuis, A. Samsonova, R. Tao, and N. Perrimon (unpublished data), results from a human proteomics study were converted to fly orthologs, which were then used to create an RNAi library for cell-based screening. Results were analyzed and integrated using enrichment and protein complex-based approaches.

Figure 2

Functional genomics workflow example two. In this workflow based on Kwon et al. (2013), known components of the Hippo signaling transduction pathway were tagged and used for mass spectrometry-based discovery of protein complexes. Results were then compared with existing complex and interaction data to assess quality and functionally tested using RNAi.