Enhanced Orthology data in FlyBase
As of the FB2016_02 release, FlyBase has incorporated orthology data from the DRSC Integrative Ortholog Prediction Tool (DIOPT). The DIOPT dataset integrates ortholog predictions for eight model organisms from ten individual tools. This approach provides a streamlined method for comparison of orthology predictions originating from different algorithms based on sequence homology, phylogenetic trees, and functional similarity. (Also see here and here.) DIOPT data are now searchable directly in FlyBase through the new ‘Orthologs’ tab of our QuickSearch tool, and are shown explicitly within the ‘Orthologs’ section of D. melanogaster Gene Reports.
The new QuickSearch tab can be used to quickly search for orthologs of genes from D. melanogaster, human, mouse, frog, zebrafish, worm, budding yeast and fission yeast. Simply select the input species, enter one or more gene symbols or IDs, then select one or more output species. Where the input species is D. melanogaster, there is a choice between searching the new DIOPT data or our existing OrthoDB-derived orthology calls. The OrthoDB-specific dataset, as implemented in FlyBase, comprises ~40 species, biased towards those that are closely related to D. melanogaster and arranged into 5 ‘orthology groups’. Researchers interested in orthology relationships between Drosophila species or related Diptera, for example, are directed towards this dataset.
The results page of a QuickSearch orthology search shows the list of ortholog predictions arranged by species. For each gene, the official gene symbol is shown alongside links to report pages at model organism databases (MODs), NCBI, Ensembl and/or OMIM. For DIOPT-based searches, the number and list of individual ortholog prediction tools that support a given orthologous gene-pair relationship is given, together with an indication of whether the given ortholog has the highest score for the query gene and whether or not the reciprocal relationship is also true. Links are also given to an alignment between orthologous gene-pairs on the DIOPT site, and to FlyBase Gene Reports where a non-Drosophila gene has been expressed transgenically in flies. A similar presentation is used for DIOPT-based data within the ‘Orthologs’ section of D. melanogaster Gene Reports.
In addition to serving the core Drosophila community, we hope that our new orthology search tool will provide an intuitive portal to FlyBase data for non-Drosophila researchers - they can search with a human/mouse/worm (etc) gene of interest and be quickly directed to pages showing the available knowledge and reagents for the fly ortholog(s). The provision of extensive links within the results page to orthologous gene reports at MODs and other external databases will further aid inter-species/database navigation.
As usual, we welcome feedback on these new features via the Contact FlyBase form.