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Detecting transcriptionally active regions using genomic tiling arrays

Gabor Halasz1,2 email, Marinus F van Batenburg1,3 email, Joelle Perusse4 email, Sujun Hua4 email, Xiang-Jun Lu1 email, Kevin P White4,5 email and Harmen J Bussemaker1,6 email

Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, NY, 10027 USA

Integrated Program in Cellular, Molecular and Biophysical Studies, Columbia University, 630 w. 168th Street, New York, NY, 10032 USA

Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands

Department of Genetics, Yale University School of Medicine, 333 Cedar Street, PO Box 208005, New Haven, CT, 06520-8005, USA

Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, PO Box 208106, New Haven, CT, 06250-8106, USA

Center for Computational Biology and Bioinformatics, Columbia University, 1130 St. Nicholas Avenue, New York, NY, USA

author email corresponding author email

Genome Biology 2006, 7:R59doi:10.1186/gb-2006-7-7-r59

Published: 19 July 2006

Subject areas: Genome studies, Bioinformatics

Abstract

We have developed a method for interpreting genomic tiling array data, implemented as the program TranscriptionDetector. Probed loci expressed above background are identified by combining replicates in a way that makes minimal assumptions about the data. We performed medium-resolution Anopheles gambiae tiling array experiments and found extensive transcription of both coding and non-coding regions. Our method also showed improved detection of transcriptional units when applied to high-density tiling array data for ten human chromosomes.


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