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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

Additional files

Additional file 1:

A perl script containing the BioTile algorithm.

Format: PL Size: 19KB Download file

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Additional file 2:

An example dataset containing the first 5000 data points from 5 randomly selected case and control mice from the simulated data matrix.

Format: TXT Size: 713KB Download file

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Additional file 3:

An example annotation file required to run BioTile on the example dataset available in Additional File 2.

Format: TXT Size: 1KB Download file

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Additional file 4:

A readme file outlining basic instructions for running BioTile. A more detailed web based vignette is available on the project homepage.

Format: TXT Size: 2KB Download file

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Additional file 5: Figure S1:

Simulated data distributions. The distributions of mean DNA methylation log2 fold change of 20 case vs. 20 control microarrays are depicted for the distribution devoid of inserted DMRS (Null distribution) and for the hidden DMRs. Figure S2. Receiver operator characteristic curves. Receiver operator characteristic curves are plotted depicting the sensitivity (y-axis) as a function of the specificity (x-axis) to identify hidden DMRs for BioTile (a), TileMap (b), and CHARM (c).

Format: DOCX Size: 147KB Download file

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