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Bioinformatics Advance Access originally published online on January 19, 2007
Bioinformatics 2007 23(5):605-611; doi:10.1093/bioinformatics/btl683
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Comparison of human protein–protein interaction maps

Matthias E. Futschik 1,*, Gautam Chaurasia 1,2 and Hanspeter Herzel 1

1Institute for Theoretical Biology, Charité, Humboldt-Universität and 2Max-Delbrück-Centrum, Invalidenstrasse 43, 10115 Berlin, Germany

*To whom correspondence should be addressed.


  Abstract

Motivation: Large-scale mappings of protein–protein interactions have started to give us new views of the complex molecular mechanisms inside a cell. After initial projects to systematically map protein interactions in model organisms such as yeast, worm and fly, researchers have begun to focus on the mapping of the human interactome. To tackle this enormous challenge, different approaches have been proposed and pursued. While several large-scale human protein interaction maps have recently been published, their quality remains to be critically assessed.

Results: We present here a first comparative analysis of eight currently available large-scale maps with a total of over 10 000 unique proteins and 57 000 interactions included. They are based either on literature search, orthology or by yeast-two-hybrid assays. Comparison reveals only a small, but statistically significant overlap. More importantly, our analysis gives clear indications that all interaction maps imply considerable selection and detection biases. These results have to be taken into account for future assembly of the human interactome.

Availability: An integrated human interaction network called Unified Human Interactome (UniHI) is made publicly accessible at http://www.mdc-berlin.de/unihi.

Contact: m.futschik{at}biologie.hu-berlin.de

Supplementary information: Supplementary data are available at Bioinformatics online.

Received on November 3, 2006; revised on December 9, 2006; accepted on January 7, 2007

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