HAT: Hypergeometric Analysis of Tiling-arrays with application to promoter-GeneChip data |
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| Authors: | Erdogan Taskesen Renee Beekman Jeroen de Ridder Bas J Wouters Justine K Peeters Ivo P Touw Marcel JT Reinders Ruud Delwel |
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| Institution: | (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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| 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. |
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