Detecting transcriptionally active regions using genomic tiling arrays

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

¹Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, NY, 10027 USA

²Integrated Program in Cellular, Molecular and Biophysical Studies, Columbia University, 630 w. 168^thStreet, New York, NY, 10032 USA

³Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands

⁴Department of Genetics, Yale University School of Medicine, 333 Cedar Street, PO Box 208005, New Haven, CT, 06520-8005, USA

⁵Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, PO Box 208106, New Haven, CT, 06250-8106, USA

⁶Center for Computational Biology and Bioinformatics, Columbia University, 1130 St. Nicholas Avenue, New York, NY, USA

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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.