The DOI matches its Crossref record; 43 of the 43 references it cites were found in a registry or an index.
MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets
Open accessAbstract
ChIP-Seq is widely used to characterize genome-wide binding patterns of transcription factors and other chromatin-associated proteins. Although comparison of ChIP-Seq data sets is critical for understanding cell type-dependent and cell state-specific binding, and thus the study of cell-specific gene regulation, few quantitative approaches have been developed. Here, we present a simple and effective method, MAnorm, for quantitative comparison of ChIP-Seq data sets describing transcription factor binding sites and epigenetic modifications. The quantitative binding differences inferred by MAnorm showed strong correlation with both the changes in expression of target genes and the binding of cell type-specific regulators.
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Model-based Analysis of ChIP-Seq (MACS)
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Different Neuronal Activity Patterns Induce Different Gene Expression Programs
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“For the purposes of visualization, read densities were normalized by scaling such that mean read densities for common ChIP-seq peaks were equal to one another, similar to the approach of MAnorm (Shao et al., 2012).”
The HD iPSC Consortium, Lim, R. G., Salazar, L. L., Wilton, D. K., King, A. R., Stocksdale, J. T., Sharifabad, D., Lau, A. L., Stevens, B., Reidling, J. C., et al. (2017) · Nature Neuroscience · doi:10.1038/nn.4532 · Cited by 221
Metadata
- Authors
- Shao, Z., Zhang, Y., Yuan, G.-C., Orkin, S. H., & Waxman, D. J.
- Venue
- Genome Biology
- Published
- 2012-03-16
- Volume
- 13
- Issue
- 3
- Pages
- R16-R16
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- OpenAlex
- W2162557359
- Cited by
- 414
- References
- 43
- FWCI
- 6.74
- Type
- journal article
- Language
- en
- Open access
- gold
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