System Biology Comparison of Human Protein-Protein Interaction Maps

Motivation: Large-scale mappings of protein-protein interactions have started to give us new views of the complex molecular mecha-nisms inside a cell. After initial projects to systematically map protein interactions in model organisms such as yeast, worm and fly, re-searchers have begun to focus on the mapping of the human inter-actome. 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 cur-rently available large-scale maps with a total of over 10000 unique proteins and 57000 interactions included. They are based either on literature search, orthology or by yeast-two-hybrid assays. Compari-son 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 hu-man interactome. Availability: An integrated human interaction network called Unified Human Interactome (UniHI) is made publicly accessible at