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Wiley, FEBS Letters, 24PartB(589), p. 3866-3870, 2015

DOI: 10.1016/j.febslet.2015.11.027

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Variable reproducibility in genome-scale public data: A case study using ENCODE ChIP sequencing resource

Journal article published in 2015 by Guillaume Devailly, Anna Mantsoki, Tom Michoel ORCID, Anagha Joshi
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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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.