Identifying hubs in protein interaction networks.
<h4>Background</h4>In spite of the scale-free degree distribution that characterizes most protein interaction networks (PINs), it is common to define an ad hoc degree scale that defines "hub" proteins having special topological and functional significance. This raises the conce...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2009-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19399170/pdf/?tool=EBI |
| _version_ | 1818836388728012800 |
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| author | Ravishankar R Vallabhajosyula Deboki Chakravarti Samina Lutfeali Animesh Ray Alpan Raval |
| author_facet | Ravishankar R Vallabhajosyula Deboki Chakravarti Samina Lutfeali Animesh Ray Alpan Raval |
| author_sort | Ravishankar R Vallabhajosyula |
| collection | DOAJ |
| description | <h4>Background</h4>In spite of the scale-free degree distribution that characterizes most protein interaction networks (PINs), it is common to define an ad hoc degree scale that defines "hub" proteins having special topological and functional significance. This raises the concern that some conclusions on the functional significance of proteins based on network properties may not be robust.<h4>Methodology</h4>In this paper we present three objective methods to define hub proteins in PINs: one is a purely topological method and two others are based on gene expression and function. By applying these methods to four distinct PINs, we examine the extent of agreement among these methods and implications of these results on network construction.<h4>Conclusions</h4>We find that the methods agree well for networks that contain a balance between error-free and unbiased interactions, indicating that the hub concept is meaningful for such networks. |
| first_indexed | 2024-12-19T03:05:49Z |
| format | Article |
| id | doaj.art-07c597b50fe94d699cb56165a04ae6dc |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-19T03:05:49Z |
| publishDate | 2009-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-07c597b50fe94d699cb56165a04ae6dc2022-12-21T20:38:06ZengPublic Library of Science (PLoS)PLoS ONE1932-62032009-01-0144e534410.1371/journal.pone.0005344Identifying hubs in protein interaction networks.Ravishankar R VallabhajosyulaDeboki ChakravartiSamina LutfealiAnimesh RayAlpan Raval<h4>Background</h4>In spite of the scale-free degree distribution that characterizes most protein interaction networks (PINs), it is common to define an ad hoc degree scale that defines "hub" proteins having special topological and functional significance. This raises the concern that some conclusions on the functional significance of proteins based on network properties may not be robust.<h4>Methodology</h4>In this paper we present three objective methods to define hub proteins in PINs: one is a purely topological method and two others are based on gene expression and function. By applying these methods to four distinct PINs, we examine the extent of agreement among these methods and implications of these results on network construction.<h4>Conclusions</h4>We find that the methods agree well for networks that contain a balance between error-free and unbiased interactions, indicating that the hub concept is meaningful for such networks.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19399170/pdf/?tool=EBI |
| spellingShingle | Ravishankar R Vallabhajosyula Deboki Chakravarti Samina Lutfeali Animesh Ray Alpan Raval Identifying hubs in protein interaction networks. PLoS ONE |
| title | Identifying hubs in protein interaction networks. |
| title_full | Identifying hubs in protein interaction networks. |
| title_fullStr | Identifying hubs in protein interaction networks. |
| title_full_unstemmed | Identifying hubs in protein interaction networks. |
| title_short | Identifying hubs in protein interaction networks. |
| title_sort | identifying hubs in protein interaction networks |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19399170/pdf/?tool=EBI |
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