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Bioinformatics Advance Access originally published online on December 12, 2006
Bioinformatics 2007 23(3):314-320; doi:10.1093/bioinformatics/btl606
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Published by Oxford University Press 2006
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.

Functional genomics via multiscale analysis: application to gene expression and ChIP-on-chip data

Gilad Lerman 1,*, Joseph McQuown 3, Alexandre Blais 4, Brian D. Dynlacht 4,5, Guangliang Chen 1 and Bud Mishra 2,4

1 Department of Mathematics, University of Minnesota 127 Vincent Hall, 206 Church St. S.E., Minneapolis, MN 55455, USA
2 Courant Institute of Mathematical Sciences, New York University 251 Mercer Street, New York, NY, 10012, USA
3 Department of Applied Mathematics and Statistics, State University of New York Stony Brook, NY 11794, USA
4 NYU School of Medicine 550 First Avenue, New York, NY, 10016, USA
5 NYU Cancer Institute 550 First Avenue, New York, NY, 10016, USA

*To whom correspondence should be addressed.


  Abstract

We present a fast, versatile and adaptive-multiscale algorithm for analyzing a wide-variety of DNA microarray data. Its primary application is in normalization of array data as well as subsequent identification of ‘enriched targets’, e.g. differentially expressed genes in expression profiling arrays and enriched sites in ChIP-on-chip experimental data.

We show how to accommodate the unique characteristics of ChIP-on-chip data, where the set of ‘enriched targets’ is large, asymmetric and whose proportion to the whole data varies locally.

Contact: lerman{at}umn.edu

Supplementary information: Supplementary figures, related preprint, free software as well as our raw DNA microarray data with PCR validations are available at http://www.math.umn.edu/~lerman/supp/bioinfo06 as well as Bioinformatics online.

Associate Editor: John Quackenbush

Received on May 2, 2006; revised on November 8, 2006; accepted on November 23, 2006

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