DNA methylation profiles of human active and inactive X chromosomes.
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Cites background from "DNA methylation profiles of human a..."
...The association between mono-allelic gene expression and DNA methylation has long been recognized, both in the context of X-inactivation in females (Boggs et al. 2002; Sharp et al. 2011) and in parent-of-origin determined genomic imprinting (Ferguson-Smith 2011), but now also in the mono-allelic expression of non-imprinted autosomal loci (Harris et al....
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...…mono-allelic gene expression and DNA methylation has long been recognized, both in the context of X-inactivation in females (Boggs et al. 2002; Sharp et al. 2011) and in parent-of-origin determined genomic imprinting (Ferguson-Smith 2011), but now also in the mono-allelic expression of…...
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References
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"DNA methylation profiles of human a..." refers methods in this paper
...…across all samples 0.2 were removed from further analyses, and a moderated t-test (Smyth 2004) was conducted to identify probes that showed significantly different methylation between 45,XMAT and 45,XPATsamples using a 5% false discovery rate (FDR) correction (Benjamini and Hochberg 1995)....
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12,142 citations
"DNA methylation profiles of human a..." refers methods in this paper
...All statistical analyses were performed using software from the Bioconductor project (Gentleman et al. 2004)....
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11,864 citations
"DNA methylation profiles of human a..." refers methods in this paper
...…distinctions between subgroups, probes with a standard deviation across all samples 0.2 were removed from further analyses, and a moderated t-test (Smyth 2004) was conducted to identify probes that showed significantly different methylation between 45,XMAT and 45,XPATsamples using a 5% false…...
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8,324 citations
"DNA methylation profiles of human a..." refers methods in this paper
...We applied quantile normalization (Bolstad et al. 2003) to the raw data and filtered outlier probes to remove low-quality data points (Sharp et al. 2010)....
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4,978 citations
"DNA methylation profiles of human a..." refers methods in this paper
...For MEME analysis, all CGIs on the X chromosome were ranked based on their mean probe log2 ratio, and the top and bottom 5% tails of this distribution were tested for enriched motifs 5–20 bp in size....
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...Although MEME analysis at genes subject to XCI, with 50% of genes escaping XCI showing a difference in log2 0.39....
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...MEME (Bailey and Elkan1994) and DRIM (Eden et al. 2007) were used to search for sequence motifs enriched in CGIs that showed extreme gains or losses of methylation....
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