Journal
GENOME BIOLOGY
Volume 13, Issue 3, Pages -Publisher
BMC
DOI: 10.1186/gb-2012-13-3-r16
Keywords
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Funding
- NHGRI NIH HHS [R01 HG005085-02, R01 HG005085] Funding Source: Medline
- NIDDK NIH HHS [R01 DK033765] Funding Source: Medline
- NATIONAL HUMAN GENOME RESEARCH INSTITUTE [R01HG005085] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES [R01DK033765] Funding Source: NIH RePORTER
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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.
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