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

K. Van Deun, H. Hoijtink, L. Thorrez, L. Van Lommel, F. Schuit, I. Van Mechelen

Research output: Contribution to journalArticleScientificpeer-review

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/.
Original languageEnglish
Pages (from-to)2588-2594
JournalBMC Bioinformatics
Volume25
Issue number19
DOIs
Publication statusPublished - 2009
Externally publishedYes

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Selectivity
Bayesian Approach
Union
Intersection
Tissue
Gene
Genes
Testing
Bayesian Methods
MATLAB
Quantify
Availability
Simulation Study
Unknown
Target
Software

Cite this

Van Deun, K. ; Hoijtink, H. ; Thorrez, L. ; Van Lommel, L. ; Schuit, F. ; Van Mechelen, I. / Testing the hypothesis of tissue selectivity : The intersection-union test and a Bayesian approach. In: BMC Bioinformatics. 2009 ; Vol. 25, No. 19. pp. 2588-2594.
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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/.",
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Van Deun, K, Hoijtink, H, Thorrez, L, Van Lommel, L, Schuit, F & Van Mechelen, I 2009, 'Testing the hypothesis of tissue selectivity: The intersection-union test and a Bayesian approach', BMC Bioinformatics, vol. 25, no. 19, pp. 2588-2594. https://doi.org/10.1093/bioinformatics/btp439

Testing the hypothesis of tissue selectivity : The intersection-union test and a Bayesian approach. / Van Deun, K.; Hoijtink, H.; Thorrez, L.; Van Lommel, L.; Schuit, F.; Van Mechelen, I.

In: BMC Bioinformatics, Vol. 25, No. 19, 2009, p. 2588-2594.

Research output: Contribution to journalArticleScientificpeer-review

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T2 - The intersection-union test and a Bayesian approach

AU - Van Deun, K.

AU - Hoijtink, H.

AU - Thorrez, L.

AU - Van Lommel, L.

AU - Schuit, F.

AU - Van Mechelen, I.

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AB - 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/.

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