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MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

Zhen Shao12, Yijing Zhang3, Guo-Cheng Yuan1, Stuart H Orkin124* and David J Waxman3*

Author Affiliations

1 Departments of Pediatric Oncology and Computational Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA

2 Division of Pediatric Hematology-Oncology, The Karp Family Research Laboratories, Children's Hospital, 300 Longwood Ave, Boston, MA 02115, USA

3 Division of Cell and Molecular Biology, Department of Biology, Boston University, 5 Cummington Street, Boston, MA 02215, USA

4 Harvard Stem Cell Institute and the Howard Hughes Medical Institute, 1 Blackfan Circle, Karp Research Building, Children's Hospital, Boston, MA 02115, USA

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Genome Biology 2012, 13:R16  doi:10.1186/gb-2012-13-3-r16

Published: 16 March 2012


ChIP-Seq is widely used to characterize genome-wide binding patterns of transcription factors and other chromatin-associated proteins. Although comparison of ChIP-Seq data sets is critical for understanding cell type-dependent and cell state-specific binding, and thus the study of cell-specific gene regulation, few quantitative approaches have been developed. Here, we present a simple and effective method, MAnorm, for quantitative comparison of ChIP-Seq data sets describing transcription factor binding sites and epigenetic modifications. The quantitative binding differences inferred by MAnorm showed strong correlation with both the changes in expression of target genes and the binding of cell type-specific regulators.