Abstract
Drosophila melanogaster is a well-established model organism that is widely used in genetic studies. This species enjoys the availability of a wide range of research tools, well-annotated reference databases and highly similar gene circuitry to other insects. To facilitate molecular mechanism studies in Drosophila, we present the Predicted Drosophila Interactome Resource (PDIR), a database of high-quality predicted functional gene interactions. These interactions were inferred from evidence in 10 public databases providing information for functional gene interactions from diverse perspectives. The current version of PDIR includes 102 835 putative functional associations with balanced sensitivity and specificity, which are expected to cover 22.56% of all Drosophila protein interactions. This set of functional interactions is a good reference for hypothesis formulation in molecular mechanism studies. At the same time, these interactions also serve as a high-quality reference interactome for gene set linkage analysis (GSLA), which is a web tool for the interpretation of the potential functional impacts of a set of changed genes observed in transcriptomics analyses. In a case study, we show that the PDIR/GSLA system was able to produce a more comprehensive and concise interpretation of the collective functional impact of multiple simultaneously changed genes compared with the widely used gene set annotation tools, including PANTHER and David. PDIR and its associated GSLA service can be accessed at http://drosophila.biomedtzc.cn.
Highlights
Drosophila melanogaster, known as the fruit fly, is one of the most commonly used model organisms and has been widely studied for more than a century [1, 2]
We attempt to predict functional associations that are as strong as protein interactions [14]
In addition to protein–protein interactions, six types of other evidence suggesting functional associations between genes from different biological perspectives were collected from seven databases, which include Coxpresdb [22], GOC [23], Compartments [24], IDDI [25], Pfam [26], DIOPT [27] and Inparanoid [28] (Figure 1)
Summary
Drosophila melanogaster, known as the fruit fly, is one of the most commonly used model organisms and has been widely studied for more than a century [1, 2]. The short life cycle of 12 days, ease of maintenance, low cost and abundance of genetic tools in Drosophila have made it a leading model in genetics research. Drosophila shares many features, genes and pathways with mammalian systems [1]. It has been widely used for research in development [3], brain disease [4] and cancer treatment [5]. The availability of abundant and complicated omics data brings both an unprecedented opportunity to comprehensively describe the physiological status of study subjects at the molecular level and, at the same time, an unparalleled challenge to elucidate the underlying design logic of the physiological processes from these comprehensive molecular-level descriptions
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