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A Genome-Wide Gene Function Prediction Resource for Drosophila melanogaster

Author

Listed:
  • Han Yan
  • Kavitha Venkatesan
  • John E Beaver
  • Niels Klitgord
  • Muhammed A Yildirim
  • Tong Hao
  • David E Hill
  • Michael E Cusick
  • Norbert Perrimon
  • Frederick P Roth
  • Marc Vidal

Abstract

Predicting gene functions by integrating large-scale biological data remains a challenge for systems biology. Here we present a resource for Drosophila melanogaster gene function predictions. We trained function-specific classifiers to optimize the influence of different biological datasets for each functional category. Our model predicted GO terms and KEGG pathway memberships for Drosophila melanogaster genes with high accuracy, as affirmed by cross-validation, supporting literature evidence, and large-scale RNAi screens. The resulting resource of prioritized associations between Drosophila genes and their potential functions offers a guide for experimental investigations.

Suggested Citation

  • Han Yan & Kavitha Venkatesan & John E Beaver & Niels Klitgord & Muhammed A Yildirim & Tong Hao & David E Hill & Michael E Cusick & Norbert Perrimon & Frederick P Roth & Marc Vidal, 2010. "A Genome-Wide Gene Function Prediction Resource for Drosophila melanogaster," PLOS ONE, Public Library of Science, vol. 5(8), pages 1-11, August.
    • Handle: RePEc:plo:pone00:0012139
    DOI: 10.1371/journal.pone.0012139
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    References listed on IDEAS

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    1. Kristin C. Gunsalus & Hui Ge & Aaron J. Schetter & Debra S. Goldberg & Jing-Dong J. Han & Tong Hao & Gabriel F. Berriz & Nicolas Bertin & Jerry Huang & Ling-Shiang Chuang & Ning Li & Ramamurthy Mani &, 2005. "Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis," Nature, Nature, vol. 436(7052), pages 861-865, August.
    2. Beatriz Estrada & Sung E Choe & Stephen S Gisselbrecht & Sebastien Michaud & Lakshmi Raj & Brian W Busser & Marc S Halfon & George M Church & Alan M Michelson, 2006. "An Integrated Strategy for Analyzing the Unique Developmental Programs of Different Myoblast Subtypes," PLOS Genetics, Public Library of Science, vol. 2(2), pages 1-12, February.
    3. Edward M. Marcotte & Matteo Pellegrini & Michael J. Thompson & Todd O. Yeates & David Eisenberg, 1999. "A combined algorithm for genome-wide prediction of protein function," Nature, Nature, vol. 402(6757), pages 83-86, November.
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