Abstract
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 language | English |
|---|---|
| Pages (from-to) | 2588-2594 |
| Journal | BMC Bioinformatics |
| Volume | 25 |
| Issue number | 19 |
| DOIs | |
| Publication status | Published - 2009 |
| Externally published | Yes |
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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 journal › Article › Scientific › peer-review
TY - JOUR
T1 - Testing the hypothesis of tissue selectivity
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.
PY - 2009
Y1 - 2009
N2 - 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/.
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/.
U2 - 10.1093/bioinformatics/btp439
DO - 10.1093/bioinformatics/btp439
M3 - Article
VL - 25
SP - 2588
EP - 2594
JO - BMC Bioinformatics
JF - BMC Bioinformatics
SN - 1471-2105
IS - 19
ER -