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Open Access Highly Accessed Research

A first-draft human protein-interaction map

Ben Lehner and Andrew G Fraser*

Author Affiliations

The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK

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Genome Biology 2004, 5:R63  doi:10.1186/gb-2004-5-9-r63

Published: 13 August 2004

Abstract

Background

Protein-interaction maps are powerful tools for suggesting the cellular functions of genes. Although large-scale protein-interaction maps have been generated for several invertebrate species, projects of a similar scale have not yet been described for any mammal. Because many physical interactions are conserved between species, it should be possible to infer information about human protein interactions (and hence protein function) using model organism protein-interaction datasets.

Results

Here we describe a network of over 70,000 predicted physical interactions between around 6,200 human proteins generated using the data from lower eukaryotic protein-interaction maps. The physiological relevance of this network is supported by its ability to preferentially connect human proteins that share the same functional annotations, and we show how the network can be used to successfully predict the functions of human proteins. We find that combining interaction datasets from a single organism (but generated using independent assays) and combining interaction datasets from two organisms (but generated using the same assay) are both very effective ways of further improving the accuracy of protein-interaction maps.

Conclusions

The complete network predicts interactions for a third of human genes, including 448 human disease genes and 1,482 genes of unknown function, and so provides a rich framework for biomedical research.