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

Guillaume Devailly, Anna Mantsoki, Tom Michoel, Anagha Joshi

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

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.

Original languageEnglish
Pages (from-to)3866–3870
JournalFEBS Letters
Volume589
Issue number24, part B
DOIs
Publication statusPublished - 21 Dec 2015

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