Perspective abstract


Nature Methods 6, 39 - 46 (2009)
Published online: 30 December 2008 | doi:10.1038/nmeth.1284



There is an Addendum (December 2009) associated with this Perspective.

Literature-curated protein interaction datasets

Michael E Cusick1,2,9, Haiyuan Yu1,2,9, Alex Smolyar1,2, Kavitha Venkatesan1,2,8, Anne-Ruxandra Carvunis1,2,3, Nicolas Simonis1,2, Jean-François Rual1,2,8, Heather Borick1,2,8, Pascal Braun1,2, Matija Dreze1,2, Jean Vandenhaute4, Mary Galli5, Junshi Yazaki5,6, David E Hill1,2, Joseph R Ecker5,6, Frederick P Roth1,7 & Marc Vidal1,2


High-quality datasets are needed to understand how global and local properties of protein-protein interaction, or 'interactome', networks relate to biological mechanisms, and to guide research on individual proteins. In an evaluation of existing curation of protein interaction experiments reported in the literature, we found that curation can be error-prone and possibly of lower quality than commonly assumed.

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  1. Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115, USA.
  2. Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA.
  3. Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications de Grenoble (TIMC-IMAG), Unité Mixte de Recherche 5525 Centre National de la Recherche Scientifique (CNRS), Faculté de Médecine, Université Joseph Fourier, 38706 La Tronche Cedex, France.
  4. Unité de Recherche en Biologie Moléculaire, Facultés Universitaires Notre-Dame de la Paix, 61 Rue de Bruxelles, 5000 Namur, Wallonia, Belgium.
  5. Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA.
  6. Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA.
  7. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, Massachusetts 02115, USA.
  8. Present addresses: Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA (K.V.), Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA (J.-F.R.) and Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, South Carolina 29634, USA (H.B.).
  9. These authors contributed equally to this work.

Correspondence to: Marc Vidal1,2 e-mail: marc_vidal@dfci.harvard.edu

Correspondence to: Michael E Cusick1,2,9 e-mail: michael_cusick@dfci.harvard.edu



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