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Letter

Protein interaction mapping: A Drosophila case study

¹ Hybrigenics, 75014 Paris, France ² The Institut Curie/Hybrigenics Laboratory, Institut Curie, 75248 Paris, France ³ CNRS UMR 144, Institut Curie, 75248 Paris, France ⁴ Inserm U520, Institut Curie, 75248 Paris, France ⁵ Inserm U509, Institut Curie, 75248 Paris, France ⁶ Inserm U528, Institut Curie, 75248 Paris, France ⁷ CNRS UMR 218, Institut Curie, 75248 Paris, France ⁸ Section Médicale/Service de Génétique, Institut Curie, 75248 Paris, France ⁹ LGPD-IBDM, 13288 Marseille, France ¹⁰ CNRS UMR 146, Institut Curie, 91405 Orsay, France ¹¹ Department of Biology, Duke University, Durham, North Carolina 27708-1000, USA ¹² Inserm U536, Institut du Fer à Moulin, 75005 Paris, France ¹³ Inserm U114, Collège de France, 75231 Paris, France ¹⁴ Inserm UMR 384, 63 001 Clermont-Ferrand, France ¹⁵ Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA ¹⁶ CNRS UMR 7592, Institut Jacques Monod, 75251 Paris, France ¹⁷ CNRS UMR 5547 Université Paul Sabatier, 31062 Toulouse, France ¹⁸ Department of Cell Biology, UT Southwestern Medical Center, Dallas, Texas 75390-9039, USA

The Drosophila (fruit fly) model system has been instrumental in our current understanding of human biology, development, and diseases. Here, we used a high-throughput yeast two-hybrid (Y2H)-based technology to screen 102 bait proteins from Drosophila melanogaster, most of them orthologous to human cancer-related and/or signaling proteins, against high-complexity fly cDNA libraries. More than 2300 protein-protein interactions (PPI) were identified, of which 710 are of high confidence. The computation of a reliability score for each protein-protein interaction and the systematic identification of the interacting domain combined with a prediction of structural/functional motifs allow the elaboration of known complexes and the identification of new ones. The full data set can be visualized using a graphical Web interface, the PIMRider (http://pim.hybrigenics.com), and is also accessible in the PSI standard Molecular Interaction data format. Our fly Protein Interaction Map (PIM) is surprisingly different from the one recently proposed by Giot et al. with little overlap between the two data sets. Analysis of the differences in data sets and methods suggests alternative strategies to enhance the accuracy and comprehensiveness of the post-genomic generation of broad-scale protein interaction maps.

²⁰ Present address: Département de Biologie, CEA-Saclay, 91191, Gifsur-Yvette, France.

¹⁹ These authors contributed equally to this work.

²² Corresponding authors.
E-mail jcamonis{at}curie.fr; fax 33 (0)142346650.
E-mail ldaviet{at}hybrigenics.fr; fax 33 (0)158103849.

[Supplemental material is available online at www.genome.org. The interaction data described in this study have been submitted to FlyBase, BIND (accession numbers: 146576-146804 and 146805-148829 for the Drosophila head and embryo interactions, respectively), and the IMEX (International Molecular Interaction Exchange) consortium (accession numbers: IMEX0000001 and IMEX0000002 for the Drosophila embryo and head interactions, respectively). The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: M. Rosbash and P. Maroy.]

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.2659105. Article published online ahead of print in February 2004.

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