C. elegans ORFeome Version 3.1: Increasing the Coverage of ORFeome Resources With Improved Gene Predictions
- Philippe Lamesch1,2,
- Stuart Milstein1,
- Tong Hao1,
- Jennifer Rosenberg1,
- Ning Li1,
- Reynaldo Sequerra3,
- Stephanie Bosak3,
- Lynn Doucette-Stamm3,
- Jean Vandenhaute2,
- David E. Hill1, and
- Marc Vidal1,4
- 1 Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- 2 Unité de Recherche en Biologie Moléculaire, Facultés Universitaires Notre-Dame de la Paix, 5000 Namur, Belgium
- 3 Agencourt Biosciences Corporation, Beverly, Massachusetts 01915, USA
Abstract
The first version of the Caenorhabditis elegans ORFeome cloning project, based on release WS9 of Wormbase (August 1999), provided experimental verifications for ∼55% of predicted protein-encoding open reading frames (ORFs). The remaining 45% of predicted ORFs could not be cloned, possibly as a result of mispredicted gene boundaries. Since the release of WS9, gene predictions have improved continuously. To test the accuracy of evolving predictions, we attempted to PCR-amplify from a highly representative worm cDNA library and Gateway-clone ∼4200 ORFs missed earlier and for which new predictions are available in WS100 (May 2003). In this set we successfully cloned 63% of ORFs with supporting experimental data (“touched” ORFs), and 42% of ORFs with no supporting experimental evidence (“untouched” ORFs). Approximately 2000 full-length ORFs were cloned in-frame, 13% of which were corrected in their exon/intron structure relative to WS100 predictions. In total, ∼12,500 C. elegans ORFs are now available as Gateway Entry clones for various reverse proteomics (ORFeome v3.1). This work illustrates why the cloning of a complete C. elegans ORFeome, and likely the ORFeomes of other multicellular organisms, needs to be an iterative process that requires multiple rounds of experimental validation together with gradually improving gene predictions.
Footnotes
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[Supplemental material is available online at www.genome.org.]
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Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.2496804.
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↵4 Corresponding author. E-MAIL marc_vidal{at}dfci.harvard.edu; FAX (617) 632-5739.
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- Accepted June 15, 2004.
- Received February 23, 2004.
- Cold Spring Harbor Laboratory Press