Variable reproducibility in genome‐scale public data: A case study using ENCODE ChIP sequencing resource. Issue 24 (24th November 2015)

• Record Type: Journal Article
• Authors: Devailly, Guillaume; Mantsoki, Anna; Michoel, Tom; Joshi, Anagha
• Is Part Of: FEBS letters. Volume 589:Issue 24(2015) Part B
• Page Start: 3866
• Page End: 3870
• Publication Date: 2015-11-24
• Subjects: ENCODE -- encyclopaedia of DNA elements -- TFBS -- transcription factor binding site -- ChIP -- chromatin immunoprecipitation -- ChIP-seq -- ChIP followed by massively parallel sequencing -- UV -- ultraviolet -- FAANG -- functional annotation of animal genomes -- UCSC -- University of California, Santa Cruz -- TSS -- transcriptional start site -- FRiP -- Fraction of Reads in Peaks -- FPKM -- Fragments per Kilo base per Million -- Encyclopaedia of DNA element -- Chromatin immunoprecipitation sequencing -- Transcription factor -- Data integration; Biochemistry -- Periodicals; Biophysics -- Periodicals; Molecular biology -- Periodicals; Biochimie -- Périodiques; Biochemistry; Biophysics; Molecular biology; Periodicals; 572.05
• DOI: 10.1016/j.febslet.2015.11.027
• Languages: English
• ISSNs: 0014-5793

Abstract

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. Abstract : Analysis of 135 ChIP sequencing experiments from ENCODE belonging to 57 conditions with replicates. A third of conditions are discordant between replicates, and another fourth have different sensitivity. Data analysis or integration helps determine biological integrity of individual samples.