Systematic functional assessment of human protein-protein interaction maps

Genome Inform. 2006;17(1):36-45.


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.

Publication types

  • Comparative Study

MeSH terms

  • Caenorhabditis elegans Proteins / chemistry
  • Caenorhabditis elegans Proteins / metabolism
  • Caenorhabditis elegans Proteins / physiology
  • Drosophila Proteins / chemistry
  • Drosophila Proteins / metabolism
  • Drosophila Proteins / physiology
  • Humans
  • Protein Interaction Mapping*
  • Proteins / chemistry*
  • Proteins / classification
  • Proteins / metabolism*
  • Proteins / physiology
  • Saccharomyces cerevisiae Proteins / chemistry
  • Saccharomyces cerevisiae Proteins / metabolism
  • Saccharomyces cerevisiae Proteins / physiology
  • Sequence Homology, Amino Acid
  • Systems Biology*
  • Two-Hybrid System Techniques


  • Caenorhabditis elegans Proteins
  • Drosophila Proteins
  • Proteins
  • Saccharomyces cerevisiae Proteins