Title: Recognition of DNase I hypersensitive sites in multiple cell lines

Authors: Wei Chen, Liaofu Luo, Lirong Zhang, Hao Lin

Addresses: Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China. ' Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China. ' Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China. ' School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China

Abstract: DNase I hypersensitive sites (DHSs) associate with a wide variety of functional genomic elements. Successful prediction of DHSs in computational models would dramatically accelerate the annotation of the human genome. In this study, a method of Increment of Diversity with Quadratic Discriminant analysis (IDQD) is presented for DHSs prediction in K562, CD4+ T, Hela and GM06990 cell lines. The average accuracies of 10-fold cross-validation test are 98.52%, 96.50%, 99.25% and 97.58%, respectively, and the mean areas under ROC curves (auROC) are all greater than 0.90. The prediction results indicate that the IDQD method is an effective tool for DHSs recognition.

Keywords: DHSs; DNase I hypersensitive sites; IDQD; increment of diversity quadratic discriminant analysis; multiple cell lines; DHS recognition; bioinformatics.

DOI: 10.1504/IJBRA.2009.027508

International Journal of Bioinformatics Research and Applications, 2009 Vol.5 No.4, pp.378 - 384

Published online: 28 Jul 2009 *

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