Stricker, Georg ORCID: 0000-0003-2949-1758, Engelhardt, Alexander, Schulz, Daniel, Schmid, Matthias ORCID: 0000-0002-0788-0317, Tresch, Achim and Gagneur, Julien ORCID: 0000-0002-8924-8365 (2017). GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis. Bioinformatics, 33 (15). S. 2258 - 2266. OXFORD: OXFORD UNIV PRESS. ISSN 1460-2059
Full text not available from this repository.Abstract
Motivation: Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) is a widely used approach to study protein-DNA interactions. Often, the quantities of interest are the differential occupancies relative to controls, between genetic backgrounds, treatments, or combinations thereof. Current methods for differential occupancy of ChIP-Seq data rely however on binning or sliding window techniques, for which the choice of the window and bin sizes are subjective. Results: Here, we present GenoGAM (Genome-wide Generalized Additive Model), which brings the well-established and flexible generalized additive models framework to genomic applications using a data parallelism strategy. We model ChIP-Seq read count frequencies as products of smooth functions along chromosomes. Smoothing parameters are objectively estimated from the data by cross-validation, eliminating ad hoc binning and windowing needed by current approaches. GenoGAM provides base-level and region-level significance testing for full factorial designs. Application to a ChIP-Seq dataset in yeast showed increased sensitivity over existing differential occupancy methods while controlling for type I error rate. By analyzing a set of DNA methylation data and illustrating an extension to a peak caller, we further demonstrate the potential of GenoGAM as a generic statistical modeling tool for genome-wide assays.
Item Type: | Journal Article | ||||||||||||||||||||||||||||
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URN: | urn:nbn:de:hbz:38-223479 | ||||||||||||||||||||||||||||
DOI: | 10.1093/bioinformatics/btx150 | ||||||||||||||||||||||||||||
Journal or Publication Title: | Bioinformatics | ||||||||||||||||||||||||||||
Volume: | 33 | ||||||||||||||||||||||||||||
Number: | 15 | ||||||||||||||||||||||||||||
Page Range: | S. 2258 - 2266 | ||||||||||||||||||||||||||||
Date: | 2017 | ||||||||||||||||||||||||||||
Publisher: | OXFORD UNIV PRESS | ||||||||||||||||||||||||||||
Place of Publication: | OXFORD | ||||||||||||||||||||||||||||
ISSN: | 1460-2059 | ||||||||||||||||||||||||||||
Language: | English | ||||||||||||||||||||||||||||
Faculty: | Unspecified | ||||||||||||||||||||||||||||
Divisions: | Unspecified | ||||||||||||||||||||||||||||
Subjects: | no entry | ||||||||||||||||||||||||||||
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Refereed: | Yes | ||||||||||||||||||||||||||||
URI: | http://kups.ub.uni-koeln.de/id/eprint/22347 |
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