A comprehensive comparison of tools for differential ChIP-seq analysis.
A comprehensive comparison of tools for differential ChIP-seq analysis.
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DOI：
10.1093/bib/bbv110
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发表时间：
2016-11
影响因子：
9.5
通讯作者：
Herrmann C
中科院分区：
文献类型：
--
作者：
Steinhauser S;Kurzawa N;Eils R;Herrmann C
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 analysis performed, the choice of method will crucially impact the outcome.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
鉴定雌激素受体结合与乳腺癌的临床结局有关。
影响因子：
64.8
作者：
Ross-Innes, Caryn S.;Stark, Rory;Teschendorff, Andrew E.;Holmes, Kelly A.;Ali, H. Raza;Dunning, Mark J.;Brown, Gordon D.;Gojis, Ondrej;Ellis, Ian O.;Green, Andrew R.;Ali, Simak;Chin, Suet-Feung;Palmieri, Carlo;Caldas, Carlos;Carroll, Jason S.
通讯作者：
Carroll, Jason S.
影响因子：
64.5
作者：
Hah N;Danko CG;Core L;Waterfall JJ;Siepel A;Lis JT;Kraus WL
通讯作者：
Kraus WL
影响因子：
5.8
作者：
Allhoff, Manuel;Sere, Kristin;Costa, Ivan G.
通讯作者：
Costa, Ivan G.
DOI：
10.1073/pnas.1320308111
发表时间：
2014-05-27
影响因子：
11.1
作者：
He, Bing;Chen, Changya;Tan, Kai
通讯作者：
Tan, Kai