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Open Access Methodology article

HAT: Hypergeometric Analysis of Tiling-arrays with application to promoter-GeneChip data

Erdogan Taskesen12, Renee Beekman1, Jeroen de Ridder234, Bas J Wouters1, Justine K Peeters1, Ivo P Touw1, Marcel JT Reinders23 and Ruud Delwel1*

Author Affiliations

1 Department of Hematology, Erasmus University Medical Center, Rotterdam, 3015 GE, the Netherlands

2 Delft Bioinformatics Lab (DBL), Delft University of Technology, Delft, 2628 CD, the Netherlands

3 Netherlands Bioinformatics Centre (NBIC), the Netherlands

4 Bioinformatics and Statistics, Department Molecular Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands

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BMC Bioinformatics 2010, 11:275  doi:10.1186/1471-2105-11-275

Published: 21 May 2010

Abstract

Background

Tiling-arrays are applicable to multiple types of biological research questions. Due to its advantages (high sensitivity, resolution, unbiased), the technology is often employed in genome-wide investigations. A major challenge in the analysis of tiling-array data is to define regions-of-interest, i.e., contiguous probes with increased signal intensity (as a result of hybridization of labeled DNA) in a region. Currently, no standard criteria are available to define these regions-of-interest as there is no single probe intensity cut-off level, different regions-of-interest can contain various numbers of probes, and can vary in genomic width. Furthermore, the chromosomal distance between neighboring probes can vary across the genome among different arrays.

Results

We have developed Hypergeometric Analysis of Tiling-arrays (HAT), and first evaluated its performance for tiling-array datasets from a Chromatin Immunoprecipitation study on chip (ChIP-on-chip) for the identification of genome-wide DNA binding profiles of transcription factor Cebpa (used for method comparison). Using this assay, we can refine the detection of regions-of-interest by illustrating that regions detected by HAT are more highly enriched for expected motifs in comparison with an alternative detection method (MAT). Subsequently, data from a retroviral insertional mutagenesis screen were used to examine the performance of HAT among different applications of tiling-array datasets. In both studies, detected regions-of-interest have been validated with (q)PCR.

Conclusions

We demonstrate that HAT has increased specificity for analysis of tiling-array data in comparison with the alternative method, and that it accurately detects regions-of-interest in two different applications of tiling-arrays. HAT has several advantages over previous methods: i) as there is no single cut-off level for probe-intensity, HAT can detect regions-of-interest at various thresholds, ii) it can detect regions-of-interest of any size, iii) it is independent of probe-resolution across the genome, and across tiling-array platforms and iv) it employs a single user defined parameter: the significance level. Regions-of-interest are detected by computing the hypergeometric-probability, while controlling the Family Wise Error. Furthermore, the method does not require experimental replicates, common regions-of-interest are indicated, a sequence-of-interest can be examined for every detected region-of-interest, and flanking genes can be reported.