Deducing topology of protein-protein interaction networks from experimentally measured sub-networks

• Main Authors: MacLellan W Robb, Han Zhangang, Vondriska Thomas M, Yang Ling, Weiss James N, Qu Zhilin
• Format: Article
• Language: English
• Published: BMC 2008-07-01
• Series: BMC Bioinformatics
• Online Access: http://www.biomedcentral.com/1471-2105/9/301

<p>Abstract</p> <p>Background</p> <p>Protein-protein interaction networks are commonly sampled using yeast two hybrid approaches. However, whether topological information reaped from these experimentally-measured sub-networks can be extrapolated to complete protein-protein interaction networks is unclear.</p> <p>Results</p> <p>By analyzing various experimental protein-protein interaction datasets, we found that they are not random samples of the parent networks. Based on the experimental bait-prey behaviors, our computer simulations show that these non-random sampling features may affect the topological information. We tested the hypothesis that a core sub-network exists within the experimentally sampled network that better maintains the topological characteristics of the parent protein-protein interaction network. We developed a method to filter the experimentally sampled network to result in a core sub-network that more accurately reflects the topology of the parent network. These findings have fundamental implications for large-scale protein interaction studies and for our understanding of the behavior of cellular networks.</p> <p>Conclusion</p> <p>The topological information from experimental measured networks network <it>as is </it>may not be the correct source for topological information about the parent protein-protein interaction network. We define a core sub-network that more accurately reflects the topology of the parent network.</p>