Peak calling

Peak calling是一種用於鑑定經染色質免疫沉澱-測序或MeDIP-測序實驗後所得到的比對讀段富集在基因組哪些區域中的一種計算方法^[1]。當免疫沉澱的蛋白質是一種轉錄因子時，那麼DNA的富集區域就是這種它的轉錄因子結合位點（TFBS）。主流的Peak calling軟件有MACS^[2]等。

Peak calling可應用於轉錄組/外顯組測序，亦可用於對MeRIP-測序^[3]或m⁶A-測序^[4]的RNA表觀基因組測序數據進行分析；利用如exomePeak等的軟件程序，可檢測出轉錄後RNA修飾位點^[5]。

另見

染色質免疫沉澱-測序
DNA測序
Peak calling軟件調查：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.

參考文獻

[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. （原始內容存檔於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. （原始內容存檔於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.

[1]

[2]

[3]

[4]

[5]