A comprehensive comparison of tools for differential ChIP-seq analysis

Briefings in Bioinformatics
Sebastian SteinhauserCarl Herrmann

Abstract

ChIP-seq has become a widely adopted genomic assay in recent years to determine binding sites for transcription factors or enrichments for specific histone modifications. Beside detection of enriched or bound regions, an important question is to determine differences between conditions. While this is a common analysis for gene expression, for which a large number of computational approaches have been validated, the same question for ChIP-seq is particularly challenging owing to the complexity of ChIP-seq data in terms of noisiness and variability. Many different tools have been developed and published in recent years. However, a comprehensive comparison and review of these tools is still missing. Here, we have reviewed 14 tools, which have been developed to determine differential enrichment between two conditions. They differ in their algorithmic setups, and also in the range of applicability. Hence, we have benchmarked these tools on real data sets for transcription factors and histone modifications, as well as on simulated data sets to quantitatively evaluate their performance. Overall, there is a great variety in the type of signal detected by these tools with a surprisingly low level of agreement. Depending on the type of a...Continue Reading

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Citations

Jul 22, 2019·BMC Research Notes·Thomas FauxLaura L Elo
May 12, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Ignacio J TripodiRobin D Dowell
Apr 23, 2020·Frontiers in Oncology·Guillermo de Anda-Jáuregui, Enrique Hernández-Lemus
Sep 18, 2020·BMC Bioinformatics·Nathaniel P Delos SantosChristopher Benner
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Nov 20, 2020·Genome Research·Shiqi TuZhen Shao
Sep 24, 2020·BMC Bioinformatics·Hayato AnzawaKengo Kinoshita
Dec 30, 2021·Briefings in Bioinformatics·Jeremiah SuryatenggaraMahmoud A Bassal

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Datasets Mentioned

BETA
GSE59530
GSM1241757
GSM1383864

Methods Mentioned

BETA
FAIRE-seq
immunoprecipitation
ChIP
ChIP-seq
RNA-seq

Software Mentioned

groHMM
PePr
GREAT
nb
diffBind
HOMER
Manorm
MultiGPS
EROI
IRanges

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