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

by: Haiyuan Yu, Philip M Kim, Emmett Sprecher, Valery Trifonov, Mark Gerstein

PLoS Computational Biology, Vol. 3, No. 4. (1 April 2007), e59.

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摘要

It has been a long-standing goal in systems biology to find relations between the topological properties and functional features of protein networks. However, most of the focus in network studies has been on highly connected proteins (“hubs”). As a complementary notion, it is possible to define bottlenecks as proteins with a high betweenness centrality (i.e., network nodes that have many “shortest paths” going through them, analogous to major bridges and tunnels on a highway map). Bottlenecks are, in fact, key connector proteins with surprising functional and dynamic properties. In particular, they are more likely to be essential proteins. In fact, in regulatory and other directed networks, betweenness (i.e., “bottleneck-ness”) is a much more significant indicator of essentiality than degree (i.e., “hub-ness”). Furthermore, bottlenecks correspond to the dynamic components of the interaction network—they are significantly less well coexpressed with their neighbors than nonbottlenecks, implying that expression dynamics is wired into the network topology.

@article{citeulike:1263147, abstract = {It has been a long-standing goal in systems biology to find relations between the topological properties and functional features of protein networks. However, most of the focus in network studies has been on highly connected proteins (\&\#8220;hubs\&\#8221;). As a complementary notion, it is possible to define bottlenecks as proteins with a high betweenness centrality (i.e., network nodes that have many \&\#8220;shortest paths\&\#8221; going through them, analogous to major bridges and tunnels on a highway map). Bottlenecks are, in fact, key connector proteins with surprising functional and dynamic properties. In particular, they are more likely to be essential proteins. In fact, in regulatory and other directed networks, betweenness (i.e., \&\#8220;bottleneck-ness\&\#8221;) is a much more significant indicator of essentiality than degree (i.e., \&\#8220;hub-ness\&\#8221;). Furthermore, bottlenecks correspond to the dynamic components of the interaction network\&\#8212;they are significantly less well coexpressed with their neighbors than nonbottlenecks, implying that expression dynamics is wired into the network topology.}, author = {Yu, Haiyuan and Kim, Philip M. and Sprecher, Emmett and Trifonov, Valery and Gerstein, Mark }, citeulike-article-id = {1263147}, doi = {10.1371/journal.pcbi.0030059}, journal = {PLoS Computational Biology}, keywords = {betweeness, network, ppi, topology}, month = {April}, number = {4}, pages = {e59+}, posted-at = {2008-05-13 08:55:50}, priority = {4}, 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} }

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TY - JOUR ID - citeulike:1263147 L3 - citeulike-article-id:1263147 TI - The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics JF - PLoS Computational Biology VL - 3 IS - 4 SP - e59 N2 - It has been a long-standing goal in systems biology to find relations between the topological properties and functional features of protein networks. However, most of the focus in network studies has been on highly connected proteins (“hubs”). As a complementary notion, it is possible to define bottlenecks as proteins with a high betweenness centrality (i.e., network nodes that have many “shortest paths” going through them, analogous to major bridges and tunnels on a highway map). Bottlenecks are, in fact, key connector proteins with surprising functional and dynamic properties. In particular, they are more likely to be essential proteins. In fact, in regulatory and other directed networks, betweenness (i.e., “bottleneck-ness”) is a much more significant indicator of essentiality than degree (i.e., “hub-ness”). Furthermore, bottlenecks correspond to the dynamic components of the interaction network—they are significantly less well coexpressed with their neighbors than nonbottlenecks, implying that expression dynamics is wired into the network topology. KW - betweeness KW - network KW - ppi KW - topology AU - Yu, Haiyuan AU - Kim, Philip AU - Sprecher, Emmett AU - Trifonov, Valery AU - Gerstein, Mark PY - 2007/04/01/ UR - http://dx.doi.org/10.1371/journal.pcbi.0030059 ER -

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