Peak calling

Peak calling是一种用于鉴定经染色质免疫沉淀-测序或MeDIP-测序实验后所得到的比对读段富集在基因组哪些区域中的一种计算方法^[1]。当免疫沉淀的蛋白质是一种转录因子时，那么DNA的富集区域就是这种它的转录因子结合位点（TFBS）。主流的Peak calling软件有MACS^[2]等。

Peak calling可应用于转录组/外显组测序，亦可用于对MeRIP-测序^[3]或m⁶A-测序^[4]的RNA表观基因组测序数据进行分析；利用如exomePeak等的软件程序，可检测出转录后RNA修饰位点^[5]。

另见

染色质免疫沉淀-测序
DNA测序
Peak calling软件调查：Wilbanks, Elizabeth G.; Facciotti, Marc T.; Veenstra, Gert Jan C. Evaluation of Algorithm Performance in ChIP-Seq Peak Detection. PLoS ONE. 7 July 2010, 5 (7): e11471. doi:10.1371/journal.pone.0011471.

参考文献

[1]
Valouev A; et al. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nature Methods. September 2008, 6 (5): 829–834 [2013-12-13]. PMC 2917543 . PMID 19160518. doi:10.1038/nmeth.1246. （原始内容存档于2011-08-10）.
[2]
Feng, Jianxing; Liu, Tao; Qin, Bo; Zhang, Yong; Liu, Xiaole Shirley. Identifying ChIP-seq enrichment using MACS. Nature Protocols. 29 August 2012, 7 (9): 1728–1740. doi:10.1038/nprot.2012.101.
[3]
Meyer, Kate D.; Saletore, Yogesh; Zumbo, Paul; Elemento, Olivier; Mason, Christopher E.; Jaffrey, Samie R. Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons. Cell. 31 May 2012, 149 (7): 1635–1646. doi:10.1016/j.cell.2012.05.003.
[4]
Dominissini, Dan; Moshitch-Moshkovitz, Sharon; Schwartz, Schraga; Salmon-Divon, Mali; Ungar, Lior; Osenberg, Sivan; Cesarkas, Karen; Jacob-Hirsch, Jasmine; Amariglio, Ninette; Kupiec, Martin; Sorek, Rotem; Rechavi, Gideon. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature. 28 April 2012, 485 (7397): 201–206. doi:10.1038/nature11112.
[5]
Meng, J.; Cui, X.; Rao, M. K.; Chen, Y.; Huang, Y. Exome-based analysis for RNA epigenome sequencing data. Bioinformatics. 14 April 2013, 29 (12): 1565–1567. doi:10.1093/bioinformatics/btt171.

[1] [1]
Valouev A; et al. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nature Methods. September 2008, 6 (5): 829–834 [2013-12-13]. PMC 2917543 . PMID 19160518. doi:10.1038/nmeth.1246. （原始内容存档于2011-08-10）.

[2] [2]
Feng, Jianxing; Liu, Tao; Qin, Bo; Zhang, Yong; Liu, Xiaole Shirley. Identifying ChIP-seq enrichment using MACS. Nature Protocols. 29 August 2012, 7 (9): 1728–1740. doi:10.1038/nprot.2012.101.

[3] [3]
Meyer, Kate D.; Saletore, Yogesh; Zumbo, Paul; Elemento, Olivier; Mason, Christopher E.; Jaffrey, Samie R. Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons. Cell. 31 May 2012, 149 (7): 1635–1646. doi:10.1016/j.cell.2012.05.003.

[4] [4]
Dominissini, Dan; Moshitch-Moshkovitz, Sharon; Schwartz, Schraga; Salmon-Divon, Mali; Ungar, Lior; Osenberg, Sivan; Cesarkas, Karen; Jacob-Hirsch, Jasmine; Amariglio, Ninette; Kupiec, Martin; Sorek, Rotem; Rechavi, Gideon. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature. 28 April 2012, 485 (7397): 201–206. doi:10.1038/nature11112.

[5] [5]
Meng, J.; Cui, X.; Rao, M. K.; Chen, Y.; Huang, Y. Exome-based analysis for RNA epigenome sequencing data. Bioinformatics. 14 April 2013, 29 (12): 1565–1567. doi:10.1093/bioinformatics/btt171.

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Peak calling

另见

参考文献

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Peak calling

另见

参考文献

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