title: Variable reproducibility in genome-scale public data: A case study using ENCODE ChIP sequencing resource.
abstract: Genome-wide data is accumulating in an unprecedented way in the public domain. Re-mining this data shows great potential to generate novel hypotheses. However this approach is dependent on the quality (technical and biological) of the underlying data. Here we performed a systematic analysis of chromatin immunoprecipitation (ChIP) sequencing data of transcription and epigenetic factors from the encyclopaedia of DNA elements (ENCODE) resource to demonstrate that about one third of conditions with replicates show low concordance between replicate peak lists. This serves as a case study to demonstrate a caveat concerning genome-wide analyses and highlights a need to validate the quality of each sample before performing further associative analyses.
authors.affiliation: The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, United Kingdom.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Devailly
authors.affiliation: The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, United Kingdom.
authors.forename: Anna
authors.initials: A
authors.lastname: Mantsoki
authors.affiliation: The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, United Kingdom.
authors.forename: Tom
authors.initials: T
authors.lastname: Michoel
authors.affiliation: The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, United Kingdom.
authors.forename: Anagha
authors.initials: A
authors.lastname: Joshi
mesh_terms: D047369:Chromatin Immunoprecipitation; D030541:Databases, Genetic; D044127:Epigenesis, Genetic; D023281:Genomics / Q000379:methods*; D056464:Histone Deacetylase 2 / Q000235:genetics; D006801:Humans; D020014:K562 Cells; D016271:Proto-Oncogene Proteins c-myc / Q000235:genetics; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000378:metabolism
chemical_list: C489427:MYC protein, human; D016271:Proto-Oncogene Proteins c-myc; D014157:Transcription Factors; D056464:Histone Deacetylase 2
keywords: Chromatin immunoprecipitation sequencing; Data integration; Encyclopaedia of DNA element; Transcription factor