Enhancing the functional content of protein interaction networks
2012-02-01
Loading...
View/Download File
Persistent link to this item
Statistics
View StatisticsJournal Title
Journal ISSN
Volume Title
Title
Enhancing the functional content of protein interaction networks
Published Date
2012-02-01
Publisher
Type
Report
Abstract
Protein interaction networks are a promising type of data for studying complex biological systems. However, despite the rich information embedded in these networks, they face important data quality challenges of noise and incompleteness that adversely affect the results obtained from their analysis. Here, we explore the use of the concept of common neighborhood similarity (CNS), which is a form of local structure in networks, to address these issues. Although several CNS measures have been proposed in the literature, an understanding of their relative efficacies for the analysis of interaction networks has been lacking. We follow the framework of graph transformation to convert the given interaction network into a transformed network corresponding to a variety of CNS measures evaluated. The effectiveness of each measure is then estimated by comparing the quality of protein function predictions obtained from its corresponding transformed network with those from the original network. Using a large set of S. cerevisiae interactions, and a set of 136 GO terms, we find that several of the transformed networks produce more accurate predictions than those obtained from the original network. In particular, the HC.cont measure proposed here performs particularly well for this task. Further investigation reveals that the two major factors contributing to this improvement are the abilities of CNS measures, especially HC.cont, to prune out noisy edges and introduce new links between functionally related proteins.
Keywords
Description
Related to
Replaces
License
Series/Report Number
Funding information
Isbn identifier
Doi identifier
Previously Published Citation
Suggested citation
Pandey, Gaurav; Manocha, Sahil; Atluri, Gowtham; Kumar, Vipin. (2012). Enhancing the functional content of protein interaction networks. Retrieved from the University Digital Conservancy, https://hdl.handle.net/11299/215879.
Content distributed via the University Digital Conservancy may be subject to additional license and use restrictions applied by the depositor. By using these files, users agree to the Terms of Use. Materials in the UDC may contain content that is disturbing and/or harmful. For more information, please see our statement on harmful content in digital repositories.