Chromatin-bound protein colocalization analysis using bedGraph2Cluster and PanChIP.
Chromatin-bound protein colocalization analysis using bedGraph2Cluster and PanChIP.
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DOI：
10.1016/j.xpro.2022.101991
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发表时间：
2023-03-17
期刊：
影响因子：
--
通讯作者：
Lawrence, Michael S.
中科院分区：
文献类型：
--
作者：
Lee, Hanjun;Sanidas, Ioannis;Dyson, Nicholas J.;Lawrence, Michael S.
用于染色质免疫沉淀测序分析的计算管道可以忽略仅在基因组的子集中发生的共定位事件。在这里，我们详细介绍了一种简化的方法，用于评估共定位的染色质结合的蛋白质使用bedGraph 2Cluster和PanChIP算法。以组蛋白修饰为例，bedGraph 2Cluster对靶蛋白的染色质结合模式进行聚类分析。PanChIP然后将这些簇与染色质结合模式的参考文库进行比较，并测量峰的重叠，捕获染色质结合和共定位模式的异质性。有关本方案使用和执行的完整详细信息，请参见Sanidas et al.（2022年）。协议识别发生在基因组k-均值聚类子集中的蛋白质共定位事件，ChIP实验库实现共定位分析bedGraph 2Cluster实现标准化，峰调用和k-均值聚类PanChIP评估查询峰和7，903 ChIP-seq实验之间的重叠进行任何实验方案都需要遵守当地实验室安全和伦理的机构指南。用于染色质免疫沉淀测序分析的计算管道可以忽略仅在基因组的子集中发生的共定位事件。在这里，我们详细介绍了一种简化的方法，用于评估共定位的染色质结合的蛋白质使用bedGraph 2Cluster和PanChIP算法。以组蛋白修饰为例，bedGraph 2Cluster对靶蛋白的染色质结合模式进行聚类分析。PanChIP然后将这些簇与染色质结合模式的参考文库进行比较，并测量峰的重叠，捕获染色质结合和共定位模式的异质性。
Computational pipelines for chromatin immunoprecipitation sequencing analysis can neglect colocalization events that occur in a mere subset of the genome. Here, we detail a streamlined approach for assessing colocalization of chromatin-bound proteins using the bedGraph2Cluster and PanChIP algorithms. Using histone modifications as an example, bedGraph2Cluster performs clustering analysis on chromatin binding patterns of target proteins. PanChIP then compares these clusters with a reference library of chromatin binding patterns and measures the overlap in peaks, capturing the heterogeneity in chromatin binding and colocalization patterns. For complete details on the use and execution of this protocol, please refer to Sanidas et al. (2022). Protocol identifies protein colocalization events that occur in a subset of genome k-means clustering and a library of ChIP experiments enable colocalization analysis bedGraph2Cluster implements normalization, peak calling, and k-means clustering PanChIP assesses the overlap between query peaks and 7,903 ChIP-seq experiments Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Computational pipelines for chromatin immunoprecipitation sequencing analysis can neglect colocalization events that occur in a mere subset of the genome. Here, we detail a streamlined approach for assessing colocalization of chromatin-bound proteins using the bedGraph2Cluster and PanChIP algorithms. Using histone modifications as an example, bedGraph2Cluster performs clustering analysis on chromatin binding patterns of target proteins. PanChIP then compares these clusters with a reference library of chromatin binding patterns and measures the overlap in peaks, capturing the heterogeneity in chromatin binding and colocalization patterns.
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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
影响因子：
7
作者：
Wang S;Zang C;Xiao T;Fan J;Mei S;Qin Q;Wu Q;Li X;Xu K;He HH;Brown M;Meyer CA;Liu XS
通讯作者：
Liu XS
影响因子：
56.9
作者：
Nurk, Sergey;Koren, Sergey;Rhie, Arang;Rautiainen, Mikko;Bzikadze, Andrey V;Mikheenko, Alla;Vollger, Mitchell R;Altemose, Nicolas;Uralsky, Lev;Gershman, Ariel;Aganezov, Sergey;Hoyt, Savannah J;Diekhans, Mark;Logsdon, Glennis A;Alonge, Michael;Antonarakis, Stylianos E;Borchers, Matthew;Bouffard, Gerard G;Brooks, Shelise Y;Caldas, Gina V;Chen, Nae-Chyun;Cheng, Haoyu;Chin, Chen-Shan;Chow, William;de Lima, Leonardo G;Dishuck, Philip C;Durbin, Richard;Dvorkina, Tatiana;Fiddes, Ian T;Formenti, Giulio;Fulton, Robert S;Fungtammasan, Arkarachai;Garrison, Erik;Grady, Patrick G S;Graves-Lindsay, Tina A;Hall, Ira M;Hansen, Nancy F;Hartley, Gabrielle A;Haukness, Marina;Howe, Kerstin;Hunkapiller, Michael W;Jain, Chirag;Jain, Miten;Jarvis, Erich D;Kerpedjiev, Peter;Kirsche, Melanie;Kolmogorov, Mikhail;Korlach, Jonas;Kremitzki, Milinn;Li, Heng;Maduro, Valerie V;Marschall, Tobias;McCartney, Ann M;McDaniel, Jennifer;Miller, Danny E;Mullikin, James C;Myers, Eugene W;Olson, Nathan D;Paten, Benedict;Peluso, Paul;Pevzner, Pavel A;Porubsky, David;Potapova, Tamara;Rogaev, Evgeny I;Rosenfeld, Jeffrey A;Salzberg, Steven L;Schneider, Valerie A;Sedlazeck, Fritz J;Shafin, Kishwar;Shew, Colin J;Shumate, Alaina;Sims, Ying;Smit, Arian F A;Soto, Daniela C;Sovic, Ivan;Storer, Jessica M;Streets, Aaron;Sullivan, Beth A;Thibaud-Nissen, Francoise;Torrance, James;Wagner, Justin;Walenz, Brian P;Wenger, Aaron;Wood, Jonathan M D;Xiao, Chunlin;Yan, Stephanie M;Young, Alice C;Zarate, Samantha;Surti, Urvashi;McCoy, Rajiv C;Dennis, Megan Y;Alexandrov, Ivan A;Gerton, Jennifer L;O'Neill, Rachel J;Timp, Winston;Zook, Justin M;Schatz, Michael C;Eichler, Evan E;Miga, Karen H;Phillippy, Adam M
通讯作者：
Phillippy, Adam M
影响因子：
7
作者：
Schneider, Valerie A.;Graves-Lindsay, Tina;Church, Deanna M.
通讯作者：
Church, Deanna M.
影响因子：
14.9
作者：
Ramírez F;Dündar F;Diehl S;Grüning BA;Manke T
通讯作者：
Manke T