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

Devailly Guillaume | Zendy; Mantsoki Anna | Zendy; Michoel Tom | Zendy; Joshi Anagha | Zendy

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

Author(s) -

Devailly Guillaume,

Mantsoki Anna,

Michoel Tom,

Joshi Anagha

Publication year - 2015

Publication title -

febs letters

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 1.593

H-Index - 257

eISSN - 1873-3468

pISSN - 0014-5793

DOI - 10.1016/j.febslet.2015.11.027

Subject(s) - encode , replicate , computational biology , encyclopedia , chromatin immunoprecipitation , genome , biology , dna sequencing , public domain , computer science , genetics , data science , dna , gene , statistics , geography , promoter , mathematics , gene expression , archaeology , library science

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.

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