Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach

<p>Abstract</p> <p>Background</p> <p>Many aspects of biological functions can be modeled by biological networks, such as protein interaction networks, metabolic networks, and gene coexpression networks. Studying the statistical properties of these networks in turn allow...

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Main Authors: Luan Yihui, Nunez-Iglesias Juan, Wang Wenhui, Sun Fengzhu
Format: Article
Language:English
Published: BMC 2009-09-01
Series:BMC Bioinformatics
Online Access:http://www.biomedcentral.com/1471-2105/10/277
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spelling doaj-1544898e3b5946bc9d84416b6b4e8b1a2020-11-25T00:37:40ZengBMCBMC Bioinformatics1471-21052009-09-0110127710.1186/1471-2105-10-277Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approachLuan YihuiNunez-Iglesias JuanWang WenhuiSun Fengzhu<p>Abstract</p> <p>Background</p> <p>Many aspects of biological functions can be modeled by biological networks, such as protein interaction networks, metabolic networks, and gene coexpression networks. Studying the statistical properties of these networks in turn allows us to infer biological function. Complex statistical network models can potentially more accurately describe the networks, but it is not clear whether such complex models are better suited to find biologically meaningful subnetworks.</p> <p>Results</p> <p>Recent studies have shown that the degree distribution of the nodes is not an adequate statistic in many molecular networks. We sought to extend this statistic with 2nd and 3rd order degree correlations and developed a pseudo-likelihood approach to estimate the parameters. The approach was used to analyze the MIPS and BIOGRID yeast protein interaction networks, and two yeast coexpression networks. We showed that 2nd order degree correlation information gave better predictions of gene interactions in both protein interaction and gene coexpression networks. However, in the biologically important task of predicting functionally homogeneous modules, degree correlation information performs marginally better in the case of the MIPS and BIOGRID protein interaction networks, but worse in the case of gene coexpression networks.</p> <p>Conclusion</p> <p>Our use of dK models showed that incorporation of degree correlations could increase predictive power in some contexts, albeit sometimes marginally, but, in all contexts, the use of third-order degree correlations decreased accuracy. However, it is possible that other parameter estimation methods, such as maximum likelihood, will show the usefulness of incorporating 2nd and 3rd degree correlations in predicting functionally homogeneous modules.</p> http://www.biomedcentral.com/1471-2105/10/277
collection DOAJ
language English
format Article
sources DOAJ
author Luan Yihui
Nunez-Iglesias Juan
Wang Wenhui
Sun Fengzhu
spellingShingle Luan Yihui
Nunez-Iglesias Juan
Wang Wenhui
Sun Fengzhu
Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach
BMC Bioinformatics
author_facet Luan Yihui
Nunez-Iglesias Juan
Wang Wenhui
Sun Fengzhu
author_sort Luan Yihui
title Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach
title_short Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach
title_full Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach
title_fullStr Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach
title_full_unstemmed Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach
title_sort usefulness and limitations of dk random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach
publisher BMC
series BMC Bioinformatics
issn 1471-2105
publishDate 2009-09-01
description <p>Abstract</p> <p>Background</p> <p>Many aspects of biological functions can be modeled by biological networks, such as protein interaction networks, metabolic networks, and gene coexpression networks. Studying the statistical properties of these networks in turn allows us to infer biological function. Complex statistical network models can potentially more accurately describe the networks, but it is not clear whether such complex models are better suited to find biologically meaningful subnetworks.</p> <p>Results</p> <p>Recent studies have shown that the degree distribution of the nodes is not an adequate statistic in many molecular networks. We sought to extend this statistic with 2nd and 3rd order degree correlations and developed a pseudo-likelihood approach to estimate the parameters. The approach was used to analyze the MIPS and BIOGRID yeast protein interaction networks, and two yeast coexpression networks. We showed that 2nd order degree correlation information gave better predictions of gene interactions in both protein interaction and gene coexpression networks. However, in the biologically important task of predicting functionally homogeneous modules, degree correlation information performs marginally better in the case of the MIPS and BIOGRID protein interaction networks, but worse in the case of gene coexpression networks.</p> <p>Conclusion</p> <p>Our use of dK models showed that incorporation of degree correlations could increase predictive power in some contexts, albeit sometimes marginally, but, in all contexts, the use of third-order degree correlations decreased accuracy. However, it is possible that other parameter estimation methods, such as maximum likelihood, will show the usefulness of incorporating 2nd and 3rd degree correlations in predicting functionally homogeneous modules.</p>
url http://www.biomedcentral.com/1471-2105/10/277
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