Peak calling: Difference between revisions
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'''Peak calling''' is a computational method used to identify areas in a [[genome]] that have been enriched with [[DNA sequencing|aligned reads]] as a consequence of performing a [[Chip-Sequencing]] or MeDIPseq experiment. These areas are those where a protein interacts with [[DNA]].<ref>{{cite journal |author=Valouev A, ''et al.'' |title=Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data |journal=Nature Methods |volume=6 |issue=5 |pages=829–834 |year=2008 |month=September |pmc=2917543 |url=http://www.nature.com/nmeth/journal/v6/n11s/full/nmeth.1371.html |pmid=19160518 |doi=10.1038/nmeth.1246}}</ref> When the protein is a [[transcription factor]], the enriched area is its [[transcription factor binding site]] (TFBS). Popular software programs include MACS <ref>{{cite journal|last=Feng|first=Jianxing|coauthors=Liu, Tao; Qin, Bo; Zhang, Yong; Liu, Xiaole Shirley|title=Identifying ChIP-seq enrichment using MACS|journal=Nature Protocols|date=29 August 2012|volume=7|issue=9|pages=1728–1740|doi=10.1038/nprot.2012.101}}</ref>. |
'''Peak calling''' is a computational method used to identify areas in a [[genome]] that have been enriched with [[DNA sequencing|aligned reads]] as a consequence of performing a [[Chip-Sequencing]] or MeDIPseq experiment. These areas are those where a protein interacts with [[DNA]].<ref>{{cite journal |author=Valouev A, ''et al.'' |title=Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data |journal=Nature Methods |volume=6 |issue=5 |pages=829–834 |year=2008 |month=September |pmc=2917543 |url=http://www.nature.com/nmeth/journal/v6/n11s/full/nmeth.1371.html |pmid=19160518 |doi=10.1038/nmeth.1246}}</ref> When the protein is a [[transcription factor]], the enriched area is its [[transcription factor binding site]] (TFBS). Popular software programs include MACS <ref>{{cite journal|last=Feng|first=Jianxing|coauthors=Liu, Tao; Qin, Bo; Zhang, Yong; Liu, Xiaole Shirley|title=Identifying ChIP-seq enrichment using MACS|journal=Nature Protocols|date=29 August 2012|volume=7|issue=9|pages=1728–1740|doi=10.1038/nprot.2012.101}}</ref>, etc.. Please see <ref>{{cite journal|last=Wilbanks|first=Elizabeth G.|coauthors=Facciotti, Marc T.; Veenstra, Gert Jan C.|title=Evaluation of Algorithm Performance in ChIP-Seq Peak Detection|journal=PLoS ONE|date=7 July 2010|volume=5|issue=7|pages=e11471|doi=10.1371/journal.pone.0011471}}</ref> for a survey of the ChIPseq peak callers. |
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Peak calling may apply to RNA epigenome sequencing data from MeRIPseq <ref>{{cite journal|last=Meyer|first=Kate D.|coauthors=Saletore, Yogesh; Zumbo, Paul; Elemento, Olivier; Mason, Christopher E.; Jaffrey, Samie R.|title=Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons|journal=Cell|date=31 May 2012|volume=149|issue=7|pages=1635–1646|doi=10.1016/j.cell.2012.05.003}}</ref> or m6A-seq <ref>{{cite journal|last=Dominissini|first=Dan|coauthors=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|title=Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq|journal=Nature|date=28 April 2012|volume=485|issue=7397|pages=201–206|doi=10.1038/nature11112}}</ref> for detection of post-transcriptional RNA modification sites with software programs, such as [[exomePeak]]. |
Peak calling may apply to RNA epigenome sequencing data from MeRIPseq <ref>{{cite journal|last=Meyer|first=Kate D.|coauthors=Saletore, Yogesh; Zumbo, Paul; Elemento, Olivier; Mason, Christopher E.; Jaffrey, Samie R.|title=Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons|journal=Cell|date=31 May 2012|volume=149|issue=7|pages=1635–1646|doi=10.1016/j.cell.2012.05.003}}</ref> or m6A-seq <ref>{{cite journal|last=Dominissini|first=Dan|coauthors=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|title=Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq|journal=Nature|date=28 April 2012|volume=485|issue=7397|pages=201–206|doi=10.1038/nature11112}}</ref> for detection of post-transcriptional RNA modification sites with software programs, such as [[exomePeak]]. |
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Revision as of 21:58, 18 August 2013
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.
Peak calling may apply to RNA epigenome sequencing data from MeRIPseq [4] or m6A-seq [5] for detection of post-transcriptional RNA modification sites with software programs, such as exomePeak.
See also
References
- ^ Valouev A; et al. (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.
{{cite journal}}: Explicit use of et al. in:|author=(help); Unknown parameter|month=ignored (help) - ^ Feng, Jianxing (29 August 2012). "Identifying ChIP-seq enrichment using MACS". Nature Protocols. 7 (9): 1728–1740. doi:10.1038/nprot.2012.101.
{{cite journal}}: Unknown parameter|coauthors=ignored (|author=suggested) (help) - ^ Wilbanks, Elizabeth G. (7 July 2010). "Evaluation of Algorithm Performance in ChIP-Seq Peak Detection". PLoS ONE. 5 (7): e11471. doi:10.1371/journal.pone.0011471.
{{cite journal}}: Unknown parameter|coauthors=ignored (|author=suggested) (help)CS1 maint: unflagged free DOI (link) - ^ Meyer, Kate D. (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.
{{cite journal}}: Unknown parameter|coauthors=ignored (|author=suggested) (help); no-break space character in|coauthors=at position 69 (help); no-break space character in|first=at position 5 (help) - ^ Dominissini, Dan (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.
{{cite journal}}: Unknown parameter|coauthors=ignored (|author=suggested) (help)
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