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Title |
Adaptive thresholds to detect differentially expressed genes in microarray data |
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Authors |
Yutaka Fukuoka1*, Hidenori Inaoka2, Makoto Noshiro2 |
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Affiliation |
1Department of Biosystems Modeling, Graduate School of Biomedical Science, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo 113-8510, Japan; 2School of Allied Health Sciences, Kitasato University, Kanagawa, Japan
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fukuoka.bsm@tmd.ac.jp; *Corresponding author
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Article Type |
Prediction Model
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Date |
Received August 04, 2011; Accepted August 04, 2011; Published August 20, 2011
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Abstract |
To detect changes in gene expression data from microarrays, a fixed threshold for fold difference is used widely. However, it is not always guaranteed that a threshold value which is appropriate for highly expressed genes is suitable for lowly expressed genes. In this study, aiming at detecting truly differentially expressed genes from a wide expression range, we proposed an adaptive threshold method (AT). The adaptive thresholds, which have different values for different expression levels, are calculated based on two measurements under the same condition. The sensitivity, specificity and false discovery rate (FDR) of AT were investigated by simulations. The sensitivity and specificity under various noise conditions were greater than 89.7% and 99.32%, respectively. The FDR was smaller than 0.27. These results demonstrated the reliability of the method.
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Keywords |
microarray, fold difference, threshold, differentially expressed genes, false discovery rate (FDR).
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Citation |
Fukuoka et al.
Bioinformation 7(1): 33-37 (2011) |
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Edited by |
P Kangueane
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ISSN |
0973-2063
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Publisher |
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License |
This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License. |