A direct comparison of protein interaction confidence assignment schemes

Background: Recent technological advances have enabled high-throughput measurements of protein-protein interactions in the cell, producing large protein interaction networks for various species at an ever-growing pace. However, common technologies like yeast two-hybrid may experience high rates of false positive detection. To combat false positive discoveries, a number of different methods have been recently developed that associate confidence scores with protein interactions. Here, we perform a rigorous comparative analysis and performance assessment among these different methods. Results: We measure the extent to which each set of confidence scores correlates with similarity of the interacting proteins in terms of function, expression, pattern of sequence conservation, and homology to interacting proteins in other species. We also employ a new metric, the Signal-toNoise Ratio of protein complexes embedded in each network, to assess the power of the different methods. Seven confidenc...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Silpa Suthram, Tomer Shlomi, Eytan Ruppin, Roded Sharan, Trey Ideker
• Keywords: BMCBI 2006, Et Al, Protein, Protein Interaction