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

@article{citeulike:2961489, abstract = {BACKGROUND: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.RESULTS: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.CONCLUSIONS:The topological information from experimental measured networks network as is 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.}, author = {Yang, Ling and Vondriska, Thomas and Han, Zhangang and Maclellan, Robb and Weiss, James and Qu, Zhilin }, citeulike-article-id = {2961489}, doi = {10.1186/1471-2105-9-301}, journal = {BMC Bioinformatics}, keywords = {interaction, modeling, network, proteomics}, number = {1}, posted-at = {2008-07-04 21:01:16}, priority = {2}, title = {Deducing topology of protein-protein interaction networks from experimentally measured sub-networks}, url = {http://dx.doi.org/10.1186/1471-2105-9-301}, volume = {9}, year = {2008} }

TY - JOUR ID - citeulike:2961489 L3 - citeulike-article-id:2961489 TI - Deducing topology of protein-protein interaction networks from experimentally measured sub-networks JF - BMC Bioinformatics VL - 9 IS - 1 N2 - BACKGROUND: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.RESULTS: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.CONCLUSIONS:The topological information from experimental measured networks network as is 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. KW - interaction KW - modeling KW - network KW - proteomics AU - Yang, Ling AU - Vondriska, Thomas AU - Han, Zhangang AU - Maclellan, Robb AU - Weiss, James AU - Qu, Zhilin PY - 2008/// UR - http://dx.doi.org/10.1186/1471-2105-9-301 ER -