The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics Export

@article{yu07, abstract = {Author SummaryA network is a graph consisting of a number of nodes with edges connecting them. Recently, network models have been widely applied to biological systems. Here, we are mainly interested in two types of biological networks: the interaction network, where nodes are proteins and edges connect interacting partners; and the regulatory network, where nodes are proteins and edges connect transcription factors and their targets. Betweenness is one of the most important topological properties of a network. It measures the number of shortest paths going through a certain node. Therefore, nodes with the highest betweenness control most of the information flow in the network, representing the critical points of the network. We thus call these nodes the "bottlenecks" of the network. Here, we focus on bottlenecks in protein networks. We find that, in the regulatory network, where there is a clear concept of information flow, protein bottlenecks indeed have a much higher tendency to be essential genes. In this type of network, betweenness is a good predictor of essentiality. Biological researchers can therefore use the betweenness as one more feature to choose potential targets for detailed analysis.}, author = {Yu, Haiyuan and Kim, Philip M. and Sprecher, Emmett and Trifonov, Valery and Gerstein, Mark}, citeulike-article-id = {1263147}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.0030059}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17447836}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17447836}, day = {20}, doi = {10.1371/journal.pcbi.0030059}, journal = {PLoS Comput Biol}, keywords = {expression-data, gene-networks, protein-interaction-networks}, month = {April}, number = {4}, pages = {e59+}, posted-at = {2009-11-01 20:39:10}, priority = {0}, publisher = {Public Library of Science}, title = {The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics}, url = {http://dx.doi.org/10.1371/journal.pcbi.0030059}, volume = {3}, year = {2007} }

TY - JOUR ID - yu07 L3 - citeulike-article-id:1263147 N2 - Author SummaryA network is a graph consisting of a number of nodes with edges connecting them. Recently, network models have been widely applied to biological systems. Here, we are mainly interested in two types of biological networks: the interaction network, where nodes are proteins and edges connect interacting partners; and the regulatory network, where nodes are proteins and edges connect transcription factors and their targets. Betweenness is one of the most important topological properties of a network. It measures the number of shortest paths going through a certain node. Therefore, nodes with the highest betweenness control most of the information flow in the network, representing the critical points of the network. We thus call these nodes the "bottlenecks" of the network. Here, we focus on bottlenecks in protein networks. We find that, in the regulatory network, where there is a clear concept of information flow, protein bottlenecks indeed have a much higher tendency to be essential genes. In this type of network, betweenness is a good predictor of essentiality. Biological researchers can therefore use the betweenness as one more feature to choose potential targets for detailed analysis. IS - 4 JF - PLoS Comput Biol TI - The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics PB - Public Library of Science VL - 3 SP - e59 KW - expression-data KW - gene-networks KW - protein-interaction-networks AU - Yu, Haiyuan AU - Kim, Philip AU - Sprecher, Emmett AU - Trifonov, Valery AU - Gerstein, Mark PY - 2007/04/20/ UR - http://dx.doi.org/10.1371/journal.pcbi.0030059 ER -