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An integrative approach to ortholog prediction for disease-focused and other functional studies

Hu, Yanhui, Flockhart, Ian, Vinayagam, Arunachalam, Bergwitz, Clemens, Berger, Bonnie, Perrimon, Norbert, Mohr, Stephanie E·2011·BMC Bioinformatics
DOI 10.1186/1471-2105-12-357PMC PMC3179972
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Abstract

Background: Mapping of orthologous genes among species serves an important role in functional genomics by allowing researchers to develop hypotheses about gene function in one species based on what is known about the functions of orthologs in other species. Several tools for predicting orthologous gene relationships are available. However, these tools can give different results and identification of predicted orthologs is not always straightforward. Results: We report a simple but effective tool, the D rosophila RNAi Screening Center I ntegrative O rtholog P rediction T ool (DIOPT; http://www.flyrnai.org/diopt), for rapid identification of orthologs. DIOPT integrates existing approaches, facilitating rapid identification of orthologs among human, mouse, zebrafish, C. elegans, Drosophila, and S. cerevisiae. As compared to individual tools, DIOPT shows increased sensitivity with only a modest decrease in specificity. Moreover, the flexibility built into the DIOPT graphical user interface allows researchers with different goals to appropriately 'cast a wide net' or limit results to highest confidence predictions. DIOPT also displays protein and domain alignments, including percent amino acid identity, for predicted ortholog pairs. This helps users identify the most appropriate matches among multiple possible orthologs. To facilitate using model organisms for functional analysis of human disease-associated genes, we used DIOPT to predict high-confidence orthologs of disease genes in Online Mendelian Inheritance in Man (OMIM) and genes in genome-wide association study (GWAS) data sets. The results are accessible through the DIOPT diseases and traits query tool (DIOPT-DIST; http://www.flyrnai.org/diopt-dist). Conclusions: DIOPT and DIOPT-DIST are useful resources for researchers working with model organisms, especially those who are interested in exploiting model organisms such as Drosophila to study the functions of human disease genes.

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Metadata

Authors
Hu, Y., Flockhart, I., Vinayagam, A., Bergwitz, C., Berger, B., Perrimon, N., & Mohr, S. E.
Venue
BMC Bioinformatics
Publisher
Springer Science and Business Media LLC
Published
2011-08-31
Volume
12
Issue
1
ISSN
1471-2105
DOI
10.1186/1471-2105-12-357
PMC
PMC3179972
Cited by
848
References
2
Language
en

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