Modeling of DNA microarray data by using physical properties of hybridization

by: GA Held, G Grinstein, Y Tu

Proceedings of the National Academy of Sciences, Vol. 100, No. 13. (24 June 2003), pp. 7575-7580.

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Abstract

A method of analyzing DNA microarray data based on the physical modeling of hybridization is presented. We demonstrate, in experimental data, a correlation between observed hybridization intensity and calculated free energy of hybridization. Then, combining hybridization rate equations, calculated free energies of hybridization, and microarray data for known target concentrations, we construct an algorithm to compute transcript concentration levels from microarray data. We also develop a method for eliminating outlying data points identified by our algorithm. We test the efficacy of these methods by comparing our results with an existing statistical algorithm, as well as by performing a cross-validation test on our model. 10.1073/pnas.0832500100

@article{Held2004, abstract = {A method of analyzing DNA microarray data based on the physical modeling of hybridization is presented. We demonstrate, in experimental data, a correlation between observed hybridization intensity and calculated free energy of hybridization. Then, combining hybridization rate equations, calculated free energies of hybridization, and microarray data for known target concentrations, we construct an algorithm to compute transcript concentration levels from microarray data. We also develop a method for eliminating outlying data points identified by our algorithm. We test the efficacy of these methods by comparing our results with an existing statistical algorithm, as well as by performing a cross-validation test on our model. 10.1073/pnas.0832500100}, author = {Held, G. A. and Grinstein, G. and Tu, Y. }, citeulike-article-id = {2682543}, doi = {http://dx.doi.org/10.1073/pnas.0832500100}, journal = {Proceedings of the National Academy of Sciences}, keywords = {statistics, tiling}, month = {June}, number = {13}, pages = {7575--7580}, posted-at = {2008-04-17 16:30:34}, priority = {2}, title = {Modeling of DNA microarray data by using physical properties of hybridization}, url = {http://dx.doi.org/10.1073/pnas.0832500100}, volume = {100}, year = {2003} }

RIS record

TY - JOUR ID - Held2004 L3 - citeulike-article-id:2682543 TI - Modeling of DNA microarray data by using physical properties of hybridization JF - Proceedings of the National Academy of Sciences VL - 100 IS - 13 SP - 7575 EP - 7580 N2 - A method of analyzing DNA microarray data based on the physical modeling of hybridization is presented. We demonstrate, in experimental data, a correlation between observed hybridization intensity and calculated free energy of hybridization. Then, combining hybridization rate equations, calculated free energies of hybridization, and microarray data for known target concentrations, we construct an algorithm to compute transcript concentration levels from microarray data. We also develop a method for eliminating outlying data points identified by our algorithm. We test the efficacy of these methods by comparing our results with an existing statistical algorithm, as well as by performing a cross-validation test on our model. 10.1073/pnas.0832500100 KW - statistics KW - tiling AU - Held, GA AU - Grinstein, G AU - Tu, Y PY - 2003/06/24/ UR - http://dx.doi.org/10.1073/pnas.0832500100 ER -

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