Get 20M+ Full-Text Papers For Less Than $1.50/day. Start a 14-Day Trial for You or Your Team.

Learn More →

Testing the hypothesis of tissue selectivity: the intersection–union test and a Bayesian approach

Testing the hypothesis of tissue selectivity: the intersection–union test and a Bayesian approach Motivation: Finding genes that are preferentially expressed in a particular tissue or condition is a problem that cannot be solved by standard statistical testing procedures. A relatively unknown procedure that can be used is the intersection–union test (IUT). However, two disadvantages of the IUT are that it is conservative and it conveys only the information of the least differing target tissue–other tissue pair.Results: We propose a Bayesian procedure that quantifies how much evidence there is in the overall expression profile for selective over-expression. In a small simulation study, it is shown that the proposed method outperforms the IUT when it comes to finding selectively expressed genes. An application to publicly available data consisting of 22 tissues shows that the Bayesian method indeed selects genes with functions that reflect the specific tissue functions. The proposed method can also be used to find genes that are underexpressed in a particular tissue.Availability: Both MATLAB and R code that implement the IUT and the Bayesian procedure in an efficient way, can be downloaded at http://ppw.kuleuven.be/okp/software/BayesianIUT/.Contact: katrijn.vandeun@psy.kuleuven.be http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Bioinformatics Oxford University Press

Testing the hypothesis of tissue selectivity: the intersection–union test and a Bayesian approach

Download PDF
7 pages

Loading next page...
 
/lp/oxford-university-press/testing-the-hypothesis-of-tissue-selectivity-the-intersection-union-eb05a0yBie

References (31)

Publisher
Oxford University Press
Copyright
© 2009 The Author(s)
ISSN
1367-4803
eISSN
1460-2059
DOI
10.1093/bioinformatics/btp439
pmid
19671693
Publisher site
See Article on Publisher Site

Abstract

Motivation: Finding genes that are preferentially expressed in a particular tissue or condition is a problem that cannot be solved by standard statistical testing procedures. A relatively unknown procedure that can be used is the intersection–union test (IUT). However, two disadvantages of the IUT are that it is conservative and it conveys only the information of the least differing target tissue–other tissue pair.Results: We propose a Bayesian procedure that quantifies how much evidence there is in the overall expression profile for selective over-expression. In a small simulation study, it is shown that the proposed method outperforms the IUT when it comes to finding selectively expressed genes. An application to publicly available data consisting of 22 tissues shows that the Bayesian method indeed selects genes with functions that reflect the specific tissue functions. The proposed method can also be used to find genes that are underexpressed in a particular tissue.Availability: Both MATLAB and R code that implement the IUT and the Bayesian procedure in an efficient way, can be downloaded at http://ppw.kuleuven.be/okp/software/BayesianIUT/.Contact: katrijn.vandeun@psy.kuleuven.be

Journal

Bioinformatics – Oxford University Press

Published: Aug 11, 2009

There are no references for this article.