Model-based Analysis of ChIP-Seq (MACS)
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References
6,488 citations
"Model-based Analysis of ChIP-Seq (M..." refers background or result in this paper
...This implies that the λlocal is critical for ChIP-Seq studies when matching control samples are not available [5,9]....
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...When applied to three human ChIP-Seq datasets to identify binding sites of FoxA1 in MCF7 cells, NRSF (neuron-restrictive silencer factor) in Jurkat T cells [8], and CTCF (CCCTC-binding factor) in CD4+ T cells [5] (summarized in Table S1 in Additional data file 1), MACS gives results superior to those produced by other published ChIP-Seq peak finding algorithms [8,11,12]....
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...and sequencing (ChIP-Seq) [5-8] have become popular tech-...
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...However, among the four recently published ChIP-Seq studies [5-8], one did not have a control sample [5] and only one of the three with control samples systematically used them to guide peak finding [8]....
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4,275 citations
Additional excerpts
...Second, ChIP-Seq data exhibit regional biases along the genome due to sequencing and mapping biases, chromatin structure and genome copy number variations [10]....
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4,166 citations
"Model-based Analysis of ChIP-Seq (M..." refers background or methods in this paper
...With the current genome coverage of most ChIP-Seq experiments, tag distribution along the genome could be modeled by a Poisson distribution [7]....
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...and sequencing (ChIP-Seq) [5-8] have become popular tech-...
[...]
...However, among the four recently published ChIP-Seq studies [5-8], one did not have a control sample [5] and only one of the three with control samples systematically used them to guide peak finding [8]....
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...[7], we find that while the ChIP-Seq efficiency of the active mark H3K4me3 remains high as pluripotent cells differentiate, that of repressive marks H3K27me3 and H3K9me3 becomes lower with differentiation (Table S2 in Additional data file 1), even though it is likely that there are more targets for these repressive marks as cells differentiate....
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2,789 citations
"Model-based Analysis of ChIP-Seq (M..." refers background or methods or result in this paper
...On the Genome Biology 2008, 9:R137 Genome Biology 2008, 9:R137 Comparison of MACS with ChIPSeq Peak Finder, FindPeaks and QuESTFigure 2 Comparison of MACS with ChIPSeq Peak Finder, FindPeaks and QuEST....
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...and sequencing (ChIP-Seq) [5-8] have become popular tech-...
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...Libraries were prepared as described in [8] using a PCR preamplification step and size selection for DNA fragments between 150 and 400 bp....
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...When applied to three human ChIP-Seq datasets to identify binding sites of FoxA1 in MCF7 cells, NRSF (neuron-restrictive silencer factor) in Jurkat T cells [8], and CTCF (CCCTC-binding factor) in CD4+ T cells [5] (summarized in Table S1 in Additional data file 1), MACS gives results superior to those produced by other published ChIP-Seq peak finding algorithms [8,11,12]....
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...For CTCF, since QuEST does not run on samples without controls, we only compared MACS to ChIPSeq Peak Finder and FindPeaks....
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1,931 citations