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

Genome Biol. 2012 Mar 16;13(3):R16. doi: 10.1186/gb-2012-13-3-r16.


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.

MeSH terms

  • Algorithms
  • Binding Sites
  • Chromatin
  • Chromatin Immunoprecipitation
  • Embryonic Stem Cells
  • Epigenesis, Genetic
  • Gene Expression Profiling
  • Genome, Human*
  • Genome-Wide Association Study
  • Genomics / methods*
  • HeLa Cells
  • Histones / genetics*
  • Histones / metabolism
  • Humans
  • K562 Cells
  • Models, Genetic*
  • Organ Specificity
  • Protein Binding
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism


  • Chromatin
  • Histones
  • Transcription Factors