Systematic Functional Assessment of Human Protein-Protein Interaction Maps

Gautam Chaurasia[1],[2] (
Hanspeter Herzel[1] (
Erich E. Wanker[2] (
Matthias E. Futschik[1] (

[1] Institute for Theoretical Biology, Humboldt-Universität, Berlin, Germany
[2] 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.

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Japanese Society for Bioinformatics