Peak calling

From Wikipedia, the free encyclopedia

Peak calling is a computational method used to identify areas in a genome that have been enriched with aligned reads as a consequence of performing a Chip-Sequencing or MeDIPseq experiment. These areas are those where a protein interacts with DNA.[1] When the protein is a transcription factor, the enriched area is its transcription factor binding site (TFBS). Popular software programs include MACS,[2] etc.. Please see [3] for a survey of the ChIPseq peak callers, and [4] for a description of practical guidelines for peak calling in ChIP-seq data.

Peak calling may be conducted on transcriptome/exome as well to RNA epigenome sequencing data from MeRIPseq [5] or m6Aseq [6] for detection of post-transcriptional RNA modification sites with software programs, such as exomePeak.[7]

See also

  • ChIP-Sequencing
  • DNA Sequencing

References

  1. ↑ Valouev A, et al. (September 2008). "Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data". Nature Methods 6 (5): 829–834. doi:10.1038/nmeth.1246. PMC 2917543. PMID 19160518. 
  2. ↑ Feng, Jianxing; Liu, Tao; Qin, Bo; Zhang, Yong; Liu, Xiaole Shirley (29 August 2012). "Identifying ChIP-seq enrichment using MACS". Nature Protocols 7 (9): 1728–1740. doi:10.1038/nprot.2012.101. 
  3. ↑ Wilbanks, Elizabeth G.; Facciotti, Marc T.; Veenstra, Gert Jan C. (7 July 2010). "Evaluation of Algorithm Performance in ChIP-Seq Peak Detection". PLoS ONE 5 (7): e11471. doi:10.1371/journal.pone.0011471. 
  4. ↑ Bailey, TL; Krajewski P, Ladunga I, Lefebvre C, Li Q, Liu T, Madrigal P, Taslim C, Zhang J. (14 November 2013). "Practical guidelines for the comprehensive analysis of ChIP-seq data". PLoS `comput Biol 9 (11): :e1003326. doi:10.1371/journal.pcbi.1003326. 
  5. ↑ Meyer, Kate D.; Saletore, Yogesh; Zumbo, Paul; Elemento, Olivier; Mason, Christopher E.; Jaffrey, Samie R. (31 May 2012). "Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons". Cell 149 (7): 1635–1646. doi:10.1016/j.cell.2012.05.003. 
  6. ↑ 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 (28 April 2012). "Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq". Nature 485 (7397): 201–206. doi:10.1038/nature11112. 
  7. ↑ Meng, J.; Cui, X.; Rao, M. K.; Chen, Y.; Huang, Y. (14 April 2013). "Exome-based analysis for RNA epigenome sequencing data". Bioinformatics 29 (12): 1565–1567. doi:10.1093/bioinformatics/btt171. 


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