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Nucleic Acids Research Advance Access originally published online on February 24, 2008
Nucleic Acids Research 2008 36(7):2395-2405; doi:10.1093/nar/gkn087
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Nucleic Acids Research, 2008, Vol. 36, No. 7 2395-2405
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Specificity of DNA microarray hybridization: characterization, effectors and approaches for data correction

Hinanit Koltai1,* and Carmiya Weingarten-Baror2

1Department of Ornamental Horticulture, ARO Volcani Center, Bet Dagan and 2Department of Neurobiology, The Weizmann Institute of Science, Rehovot, Israel

*To whom correspondence should be addressed. Tel: +972 3 9683039; Fax: +972 3 9669583; Email: hkoltai{at}agri.gov.il

Received December 23, 2007. Revised February 11, 2008. Accepted February 11, 2008.

Microarray-hybridization specificity is one of the main effectors of microarray result quality. In the present review, we suggest a definition for specificity that spans four hybridization levels, from the single probe to the microarray platform. For increased hybridization specificity, it is important to quantify the extent of the specificity at each of these levels, and correct the data accordingly. We outline possible effects of low hybridization specificity on the obtained results and list possible effectors of hybridization specificity. In addition, we discuss several studies in which theoretical approaches, empirical means or data filtration were used to identify specificity effectors, and increase the specificity of the hybridization results. However, these various approaches may not yet provide an ultimate solution; rather, further tool development is needed to enhance microarray-hybridization specificity.


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