MAnorm2 for quantitatively comparing groups of ChIP-seq samples.
MAnorm2 for quantitatively comparing groups of ChIP-seq samples.
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MAnorm2 用于定量比较 ChIP-seq 样本组。
DOI：
10.1101/gr.262675.120
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发表时间：
2021-01
期刊：
影响因子：
7
通讯作者：
Shao Z
中科院分区：
文献类型：
--
作者：
Tu S;Li M;Chen H;Tan F;Xu J;Waxman DJ;Zhang Y;Shao Z
真核基因转录受到大量染色质相关蛋白的调控，推断它们在不同细胞环境之间的差异结合位点需要对相应的染色质免疫沉淀测序（ChIP - seq）数据进行严格比较。我们介绍MAnorm2，这是一种用于定量比较多组ChIP - seq样本的新型计算工具。MAnorm2采用一种分层策略对ChIP - seq数据进行归一化，并基于经验贝叶斯框架评估ChIP - seq信号的组内变异性。在此框架下，MAnorm2能够处理样本组之间大量的差异ChIP - seq信号以及组间非常不同的整体组内变异性。通过使用一些真实的ChIP - seq数据集，我们观察到MAnorm2在差异ChIP - seq分析方面明显优于现有工具，尤其是当被比较的样本组具有明显不同的整体组内变异性时。
Eukaryotic gene transcription is regulated by a large cohort of chromatin-associated proteins, and inferring their differential binding sites between cellular contexts requires a rigorous comparison of the corresponding ChIP-seq data. We present MAnorm2, a new computational tool for quantitatively comparing groups of ChIP-seq samples. MAnorm2 uses a hierarchical strategy for normalization of ChIP-seq data and assesses within-group variability of ChIP-seq signals based on an empirical Bayes framework. In this framework, MAnorm2 allows for abundant differential ChIP-seq signals between groups of samples as well as very different global within-group variability between groups. Using a number of real ChIP-seq data sets, we observed that MAnorm2 clearly outperformed existing tools for differential ChIP-seq analysis, especially when the groups of samples being compared had distinct global within-group variability.
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DOI：
10.1038/nrm3949
发表时间：
2015-03
期刊：
Nature reviews. Molecular cell biology
影响因子：
--
作者：
Heinz S;Romanoski CE;Benner C;Glass CK
通讯作者：
Glass CK
影响因子：
64.8
作者：
Ernst, Jason;Kheradpour, Pouya;Mikkelsen, Tarjei S.;Shoresh, Noam;Ward, Lucas D.;Epstein, Charles B.;Zhang, Xiaolan;Wang, Li;Issner, Robbyn;Coyne, Michael;Ku, Manching;Durham, Timothy;Kellis, Manolis;Bernstein, Bradley E.
通讯作者：
Bernstein, Bradley E.
DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
32.4
作者：
Koues, Olivia I.;Kowalewski, Rodney A.;Chang, Li-Wei;Pyfrom, Sarah C.;Schmidt, Jennifer A.;Luo, Hong;Sandoval, Luis E.;Hughes, Tyler B.;Bednarski, Jeffrey J.;Cashen, Amanda F.;Payton, Jacqueline E.;Oltz, Eugene M.
通讯作者：
Oltz, Eugene M.
影响因子：
14.9
作者：
Lun AT;Smyth GK
通讯作者：
Smyth GK