title: Model-based analysis of ChIP-Seq (MACS).
abstract: We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available.
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115, USA.
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.forename: Clifford A
authors.initials: CA
authors.lastname: Meyer
authors.forename: Jérôme
authors.initials: J
authors.lastname: Eeckhoute
authors.forename: David S
authors.initials: DS
authors.lastname: Johnson
authors.forename: Bradley E
authors.initials: BE
authors.lastname: Bernstein
authors.forename: Chad
authors.initials: C
authors.lastname: Nusbaum
authors.forename: Richard M
authors.initials: RM
authors.lastname: Myers
authors.forename: Myles
authors.initials: M
authors.lastname: Brown
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: X Shirley
authors.initials: XS
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D051541:Hepatocyte Nuclear Factor 3-alpha / Q000032:analysis / Q000235:genetics*; D006801:Humans; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*
chemical_list: C496499:FOXA1 protein, human; D051541:Hepatocyte Nuclear Factor 3-alpha
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