RT Journal Article
SR Electronic
T1 Approximate Bayesian bisulphite sequencing analysis
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 041715
DO 10.1101/041715
A1 Owen J.L. Rackham
A1 Sarah R. Langley
A1 Thomas Oates
A1 Eleni Vradi
A1 Nathan Harmston
A1 Prashant K. Srivastava
A1 Jacques Behmoaras
A1 Petros Dellaportas
A1 Leonardo Bottolo
A1 Enrico Petretto
YR 2016
UL http://biorxiv.org/content/early/2016/02/29/041715.abstract
AB We present a Bayesian smoothing approach to detect differentially methylated regions from whole-genome bisulfite sequencing (WGBS) data. The method exploits the Integrated Nested Laplace Approximation for fast and accurate model fitting, an alternative to computationally expensive sampling-based methods. We demonstrate the approach by extensive simulation studies and WGBS of macrophages in experimental glomerulonephritis, revealing differential Ifitm3 promoter methylation in glomerulonephritis, supported by differential transcription factor binding and Ifitm3 gene expression.