title: Combining multiple ChIP-seq peak detection systems using combinatorial fusion.
abstract: BACKGROUND
  Due to the recent rapid development in ChIP-seq technologies, which uses high-throughput next-generation DNA sequencing to identify the targets of Chromatin Immunoprecipitation, there is an increasing amount of sequencing data being generated that provides us with greater opportunity to analyze genome-wide protein-DNA interactions. In particular, we are interested in evaluating and enhancing computational and statistical techniques for locating protein binding sites. Many peak detection systems have been developed; in this study, we utilize the following six: CisGenome, MACS, PeakSeq, QuEST, SISSRs, and TRLocator.
  
  
  RESULTS
  We define two methods to merge and rescore the regions of two peak detection systems and analyze the performance based on average precision and coverage of transcription start sites. The results indicate that ChIP-seq peak detection can be improved by fusion using score or rank combination.
  
  
  CONCLUSIONS
  Our method of combination and fusion analysis would provide a means for generic assessment of available technologies and systems and assist researchers in choosing an appropriate system (or fusion method) for analyzing ChIP-seq data. This analysis offers an alternate approach for increasing true positive rates, while decreasing false positive rates and hence improving the ChIP-seq peak identification process.
authors.affiliation: Laboratory for Informatics and Data Mining, Department of Computer and Information Science, Fordham University, New York, NY 10023, USA. cschweikert@cis.fordham.edu
authors.forename: Christina
authors.initials: C
authors.lastname: Schweikert
authors.forename: Stuart
authors.initials: S
authors.lastname: Brown
authors.forename: Zuojian
authors.initials: Z
authors.lastname: Tang
authors.forename: Phillip R
authors.initials: PR
authors.lastname: Smith
authors.forename: D Frank
authors.initials: DF
authors.lastname: Hsu
mesh_terms: D000465:Algorithms; D000906:Antibodies / Q000276:immunology; D047369:Chromatin Immunoprecipitation; D004247:DNA / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D011485:Protein Binding; D011506:Proteins / Q000276:immunology / Q000378:metabolism
chemical_list: D000906:Antibodies; D011506:Proteins; D004247:DNA