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BioTile, A Perl based tool for the identification of differentially enriched regions in tiling microarray data

Jerry Guintivano1, Michal Arad2, Kellie LK Tamashiro1, Todd D Gould234 and Zachary A Kaminsky1*

Author Affiliations

1 Mood Disorders Center, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, USA

2 Department of Psychiatry, University of Maryland School of Medicine, Baltimore, USA

3 Department of Pharmacology, University of Maryland School of Medicine, Baltimore, USA

4 Department of Anatomy & Neurobiology, University of Maryland School of Medicine, Baltimore, USA

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BMC Bioinformatics 2013, 14:76  doi:10.1186/1471-2105-14-76

Published: 3 March 2013

Abstract

Background

Genome-wide tiling array experiments are increasingly used for the analysis of DNA methylation. Because DNA methylation patterns are tissue and cell type specific, the detection of differentially methylated regions (DMRs) with small effect size is a necessary feature of tiling microarray ‘peak’ finding algorithms, as cellular heterogeneity within a studied tissue may lead to a dilution of the phenotypically relevant effects. Additionally, the ability to detect short length DMRs is necessary as biologically relevant signal may occur in focused regions throughout the genome.

Results

We present a free open-source Perl application, Binding Intensity Only Tile array analysis or “BioTile”, for the identification of differentially enriched regions (DERs) in tiling array data. The application of BioTile to non-smoothed data allows for the identification of shorter length and smaller effect-size DERs, while correcting for probe specific variation by inversely weighting on probe variance through a permutation corrected meta-analysis procedure employed at identified regions. BioTile exhibits higher power to identify significant DERs of low effect size and across shorter genomic stretches as compared to other peak finding algorithms, while not sacrificing power to detect longer DERs.

Conclusion

BioTile represents an easy to use analysis option applicable to multiple microarray platforms, allowing for its integration into the analysis workflow of array data analysis.

Keywords:
DNA methylation; Differentially methylated region; Tiling microarray; Algorithm; Epigenetic