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BioTile, a Perl based tool for the identification of differentially enriched regions in tiling microarray data.
Jerry Guintivano1, Michal Arad, Kellie L K Tamashiro
1Mood Disorders Center, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
BMC Bioinformatics
|March 5, 2013
Summary
BioTile is a new open-source tool for analyzing DNA methylation data from tiling arrays. It effectively identifies small and short differentially methylated regions (DMRs), improving genomic analysis.
Area of Science:
- Genomics
- Epigenetics
- Bioinformatics
Background:
- Genome-wide tiling arrays are crucial for DNA methylation analysis.
- Detecting small effect size and short differentially methylated regions (DMRs) is vital due to cellular heterogeneity.
- Existing algorithms struggle with identifying subtle or localized methylation changes.
Purpose of the Study:
- To introduce BioTile, a novel open-source Perl application for identifying differentially enriched regions (DERs) in tiling array data.
- To enhance the detection of short and small effect size DERs.
- To provide a robust tool for analyzing DNA methylation patterns.
Main Methods:
- Developed BioTile, a Perl-based application for tiling array analysis.
- Applied BioTile to non-smoothed data to preserve signal integrity.
- Utilized a permutation-corrected meta-analysis with inverse probe variance weighting to correct for probe-specific variation.
Main Results:
- BioTile successfully identifies shorter length and smaller effect-size DERs.
- The tool demonstrates higher power in detecting significant DERs with low effect size and across shorter genomic regions compared to other algorithms.
- BioTile maintains power for detecting longer DERs without compromise.
Conclusions:
- BioTile is an easy-to-use analysis tool for tiling array data.
- It is applicable to multiple microarray platforms, facilitating integration into existing workflows.
- BioTile enhances the ability to detect subtle and localized DNA methylation differences.
