Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality.
The centrality-lethality rule, which notes that high-degree nodes in a protein interaction network tend to correspond to proteins that are essential, suggests that the topological prominence of a protein in a protein interaction network may be a good predictor of its biological importance. Even thou...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2008-08-01
|
| Series: | PLoS Computational Biology |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18670624/?tool=EBI |
| _version_ | 1818984461223591936 |
|---|---|
| author | Elena Zotenko Julian Mestre Dianne P O'Leary Teresa M Przytycka |
| author_facet | Elena Zotenko Julian Mestre Dianne P O'Leary Teresa M Przytycka |
| author_sort | Elena Zotenko |
| collection | DOAJ |
| description | The centrality-lethality rule, which notes that high-degree nodes in a protein interaction network tend to correspond to proteins that are essential, suggests that the topological prominence of a protein in a protein interaction network may be a good predictor of its biological importance. Even though the correlation between degree and essentiality was confirmed by many independent studies, the reason for this correlation remains illusive. Several hypotheses about putative connections between essentiality of hubs and the topology of protein-protein interaction networks have been proposed, but as we demonstrate, these explanations are not supported by the properties of protein interaction networks. To identify the main topological determinant of essentiality and to provide a biological explanation for the connection between the network topology and essentiality, we performed a rigorous analysis of six variants of the genomewide protein interaction network for Saccharomyces cerevisiae obtained using different techniques. We demonstrated that the majority of hubs are essential due to their involvement in Essential Complex Biological Modules, a group of densely connected proteins with shared biological function that are enriched in essential proteins. Moreover, we rejected two previously proposed explanations for the centrality-lethality rule, one relating the essentiality of hubs to their role in the overall network connectivity and another relying on the recently published essential protein interactions model. |
| first_indexed | 2024-12-20T18:19:22Z |
| format | Article |
| id | doaj.art-1dfc41e3c4764ca69958bda9fabf7220 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-20T18:19:22Z |
| publishDate | 2008-08-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-1dfc41e3c4764ca69958bda9fabf72202022-12-21T19:30:17ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582008-08-0148e100014010.1371/journal.pcbi.1000140Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality.Elena ZotenkoJulian MestreDianne P O'LearyTeresa M PrzytyckaThe centrality-lethality rule, which notes that high-degree nodes in a protein interaction network tend to correspond to proteins that are essential, suggests that the topological prominence of a protein in a protein interaction network may be a good predictor of its biological importance. Even though the correlation between degree and essentiality was confirmed by many independent studies, the reason for this correlation remains illusive. Several hypotheses about putative connections between essentiality of hubs and the topology of protein-protein interaction networks have been proposed, but as we demonstrate, these explanations are not supported by the properties of protein interaction networks. To identify the main topological determinant of essentiality and to provide a biological explanation for the connection between the network topology and essentiality, we performed a rigorous analysis of six variants of the genomewide protein interaction network for Saccharomyces cerevisiae obtained using different techniques. We demonstrated that the majority of hubs are essential due to their involvement in Essential Complex Biological Modules, a group of densely connected proteins with shared biological function that are enriched in essential proteins. Moreover, we rejected two previously proposed explanations for the centrality-lethality rule, one relating the essentiality of hubs to their role in the overall network connectivity and another relying on the recently published essential protein interactions model.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18670624/?tool=EBI |
| spellingShingle | Elena Zotenko Julian Mestre Dianne P O'Leary Teresa M Przytycka Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. PLoS Computational Biology |
| title | Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. |
| title_full | Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. |
| title_fullStr | Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. |
| title_full_unstemmed | Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. |
| title_short | Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. |
| title_sort | why do hubs in the yeast protein interaction network tend to be essential reexamining the connection between the network topology and essentiality |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18670624/?tool=EBI |
| work_keys_str_mv | AT elenazotenko whydohubsintheyeastproteininteractionnetworktendtobeessentialreexaminingtheconnectionbetweenthenetworktopologyandessentiality AT julianmestre whydohubsintheyeastproteininteractionnetworktendtobeessentialreexaminingtheconnectionbetweenthenetworktopologyandessentiality AT diannepoleary whydohubsintheyeastproteininteractionnetworktendtobeessentialreexaminingtheconnectionbetweenthenetworktopologyandessentiality AT teresamprzytycka whydohubsintheyeastproteininteractionnetworktendtobeessentialreexaminingtheconnectionbetweenthenetworktopologyandessentiality |