Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data.
Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data.
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DOI：
10.3389/fgene.2014.00075
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发表时间：
2014
影响因子：
3.7
通讯作者：
de Santiago I
中科院分区：
文献类型：
--
作者：
Carroll TS;Liang Z;Salama R;Stark R;de Santiago I
随着CHIP-SEQ多路复用技术的出现和随后CHIP-SEQ吞吐量的增加，为CHIP-SEQ研究的质量评估制定工作标准受到了极大的关注。ENCODE联盟对转录因子结合和表观遗传标记的大规模分析，以及其他实验室对CHIP-SEQ的协调工作，建立了新一代CHIP-SEQ质量控制措施。然而，这些指标与通用处理步骤一起使用的情况尚未得到评估。在这项研究中，我们调查了列入黑名单和去除重复读取对已建立的芯片序列质量指标的影响，并表明这些指标的解释高度依赖于所应用的芯片序列预处理步骤。此外，我们对芯片-exo数据使用这些度量进行了第一次调查，并为调整NSC统计数据以评估芯片-exo效率提出了建议。
With the advent of ChIP-seq multiplexing technologies and the subsequent increase in ChIP-seq throughput, the development of working standards for the quality assessment of ChIP-seq studies has received significant attention. The ENCODE consortium's large scale analysis of transcription factor binding and epigenetic marks as well as concordant work on ChIP-seq by other laboratories has established a new generation of ChIP-seq quality control measures. The use of these metrics alongside common processing steps has however not been evaluated. In this study, we investigate the effects of blacklisting and removal of duplicated reads on established metrics of ChIP-seq quality and show that the interpretation of these metrics is highly dependent on the ChIP-seq preprocessing steps applied. Further to this we perform the first investigation of the use of these metrics for ChIP-exo data and make recommendations for the adaptation of the NSC statistic to allow for the assessment of ChIP-exo efficiency.
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影响因子：
4.3
作者：
Bailey T;Krajewski P;Ladunga I;Lefebvre C;Li Q;Liu T;Madrigal P;Taslim C;Zhang J
通讯作者：
Zhang J
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：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
影响因子：
30.5
作者：
Kidder, Benjamin L.;Hu, Gangqing;Zhao, Keji
通讯作者：
Zhao, Keji
影响因子：
5.8
作者：
Ramachandran, Parameswaran;Palidwor, Gareth A.;Perkins, Theodore J.
通讯作者：
Perkins, Theodore J.