Document Detail


Smoothing gene expression data with network information improves consistency of regulated genes.
MedLine Citation:
PMID:  23089828     Owner:  NLM     Status:  In-Data-Review    
Abstract/OtherAbstract:
Gene set analysis methods have become a widely used tool for including prior biological knowledge in the statistical analysis of gene expression data. Advantages of these methods include increased sensitivity, easier interpretation and more conformity in the results. However, gene set methods do not employ all the available information about gene relations. Genes are arranged in complex networks where the network distances contain detailed information about inter-gene dependencies. We propose a method that uses gene networks to smooth gene expression data with the aim of reducing the number of false positives and identify important subnetworks. Gene dependencies are extracted from the network topology and are used to smooth genewise test statistics. To find the optimal degree of smoothing, we propose using a criterion that considers the correlation between the network and the data. The network smoothing is shown to improve the ability to identify important genes in simulated data. Applied to a real data set, the smoothing accentuates parts of the network with a high density of differentially expressed genes.
Authors:
Guro Dørum; Lars Snipen; Margrete Solheim; Solve Saebo
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Publication Detail:
Type:  Journal Article     Date:  2011-08-09
Journal Detail:
Title:  Statistical applications in genetics and molecular biology     Volume:  10     ISSN:  1544-6115     ISO Abbreviation:  Stat Appl Genet Mol Biol     Publication Date:  2011  
Date Detail:
Created Date:  2012-10-23     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101176023     Medline TA:  Stat Appl Genet Mol Biol     Country:  Germany    
Other Details:
Languages:  eng     Pagination:  -     Citation Subset:  IM    
Affiliation:
Norwegian University of Life Sciences.
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