Gautam Chaurasia, (firstname.lastname@example.org)
Hanspeter Herzel (email@example.com)
Erich E. Wanker (firstname.lastname@example.org)
Matthias E. Futschik (email@example.com)
 Institute for Theoretical Biology, Humboldt-Universität, Berlin, Germany
 Max-Delbrück-Centrum for Molecular Medicine, Berlin-Buch, Berlin, Germany
Protein-protein interaction maps can contribute substantially to the discovery of protein cooperation patterns in the cell. Recently, several large-scale human protein-protein interaction maps have been generated using experimental or computational approaches. Evaluation of these maps is likely to provide a better understanding of human biology. However, careful analysis is needed, as the comparison of interaction maps of lower eukaryotes showed a surprising divergence between different maps. Here, we present a first systematic functional assessment of eight currently available large-scale human protein-protein interaction maps. The analysis shows that these maps include a large number of common proteins, but only a small number of common interactions. We detected several types of biases that need to be considered in the future utilization of these maps.