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

z3mao · 03-20-2012, 04:30 PM

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.

Package download address: http://genomebiology.com/imedia/1544...4863/supp1.zip

Both R/BASH and MATLAB versions available Please contact zhangyij@gmail.com for any questions.

Paper link: http://genomebiology.com/2012/13/3/R16/abstract

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03-20-2012, 04:30 PM	#1
z3mao Junior Member Location: boston Join Date: Nov 2011 Posts: 1	MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets 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. Package download address: http://genomebiology.com/imedia/1544...4863/supp1.zip Both R/BASH and MATLAB versions available Please contact zhangyij@gmail.com for any questions. Paper link: http://genomebiology.com/2012/13/3/R16/abstract