EGASP: collaboration through competition to find human genes

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According to the most recent estimates, the number of human genes is possibly—but not certainly—between 20,000 and 25,000. To contribute strategies to reduce this uncertainty, several groups working on computational gene prediction met recently at the Welcome Trust Sanger Institute with the goal to test and compare predictive methods of genome annotation.

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Figure 1: Measuring accuracy of gene prediction tools against expert annotations.
Figure 2: Sensitivity and specificity at the exon level of several predictions submitted to EGASP'05.

References

  1. 1

    Venter, J.C. et al. Science 291, 1304–1351 (2001).

  2. 2

    Lander, E.S. et al. Nature 409, 860–921 (2001).

  3. 3

    Rogers, J. Cold Spring Harb. Symp. Quant. Biol. 68, 1–11 (2003).

  4. 4

    International Human Genome Sequencing Consortium. Nature 431, 931–945 (2004).

  5. 5

    Brent, M.R. & Guigo, R. Curr. Opin. Struct. Biol. 14, 264–272 (2004).

  6. 6

    ENCODE Project Consortium. Science 306, 636–340 (2004).

  7. 7

    Ashurst, J.L. & Collins, J.E. Annu. Rev. Genomics Hum. Genet. 4, 69–88 (2003).

  8. 8

    Reese, M.G. et al. Genome Res. 10, 483–501 (2000).

  9. 9

    Bajic, V.B. Brief Bioinform. 1, 214228 (2000).

  10. 10

    Baldi, P., Brunak, S., Chauvin, Y., Andersen, C.A. & Nielsen, H. Bioinformatics 16, 412–424 (2000).

  11. 11

    Burset, M. & Guigo, R. Genomics 34, 353–367 (1996).

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Acknowledgements

The GENCODE annotation is mostly the effort of A. Frankish, D. Swarbreck, J. Gilbert, J. Ashurst and T. Hubbard from the Havana team at the Wellcome Trust Sanger Institute; of C. Ucla, A. Reymond and S. Antonarakis from the Faculté de Médecine Université de Genève, and of F. Denoeud, J. Lagarde and R. Guigó from the Institut Municipal d'Investigació Mèdica (IMIM) in Barcelona. P. Flicek from the European Bioinformatics Insitute and J.F. Abril from the IMIM were responsible for computing most of the accuracy measures. J. Ashurst, E. Birney, P. Good, R. Guigó and T. Hubbard participated in the organizing committee. M. Ashburner, V.B. Bajic, T. Gingeras, S. Lewis and M. Reese were members of the advisory committee. The workshop was part of the ENCODE project that is funded by the US National Institutes of Health NHGRI.

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Guigó, R., Reese, M. EGASP: collaboration through competition to find human genes. Nat Methods 2, 575–577 (2005) doi:10.1038/nmeth0805-575

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