title: diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates.
abstract: ChIP-seq is increasingly being used for genome-wide profiling of histone modification marks. It is of particular importance to compare ChIP-seq data of two different conditions, such as disease vs. control, and identify regions that show differences in ChIP enrichment. We have developed a powerful and easy to use program, called diffReps, to detect those differential sites from ChIP-seq data, with or without biological replicates. In addition, we have developed two useful tools for ChIP-seq analysis in the diffReps package: one for the annotation of the differential sites and the other for finding chromatin modification "hotspots". diffReps is developed in PERL programming language and runs on all platforms as a command line script. We tested diffReps on two different datasets. One is the comparison of H3K4me3 between two human cell lines from the ENCODE project. The other is the comparison of H3K9me3 in a discrete region of mouse brain between cocaine- and saline-treated conditions. The results indicated that diffReps is a highly sensitive program in detecting differential sites from ChIP-seq data.
authors.affiliation: Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America. li.shen@mssm.edu
authors.forename: Li
authors.initials: L
authors.lastname: Shen
authors.forename: Ning-Yi
authors.initials: NY
authors.lastname: Shao
authors.forename: Xiaochuan
authors.initials: X
authors.lastname: Liu
authors.forename: Ian
authors.initials: I
authors.lastname: Maze
authors.forename: Jian
authors.initials: J
authors.lastname: Feng
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Nestler
mesh_terms: D000465:Algorithms; D000818:Animals; D001665:Binding Sites; D002843:Chromatin / Q000187:drug effects / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D003042:Cocaine / Q000494:pharmacology; D057225:Data Mining / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones / Q000378:metabolism*; D006801:Humans; D051379:Mice; D009714:Nucleus Accumbens / Q000187:drug effects* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software; D014662:Vasoconstrictor Agents / Q000494:pharmacology
chemical_list: D002843:Chromatin; D006657:Histones; D014662:Vasoconstrictor Agents; D003042:Cocaine