Of 8268 CpG regions of ≥ 60 CpGs eligible for analysis with SOMNiBUS, we identified 131 DMRs and 125 differentially methylated genes (DMGs p-values less than Bonferroni-corrected threshold of 6.05–06 controlling family-wise error rate at 0.05 1.6% of the regions). We compared the results obtained by SOMNiBUS and bumphunter. Pathway enrichment analysis was performed with ingenuity pathway analysis (IPA). We separated the resulting sequencing data into regions with dense CpG data, and differentially methylated regions (DMRs) were inferred with the SOMNiBUS region-level test, adjusted for age. Purified CD4+ T lymphocytes of 9 SSc and 4 control females were sequenced using WGBS. Using SOMNiBUS, we re-analyzed WGBS data previously analyzed using bumphunter, an approach that initially fits single CpG associations, to contrast DNA methylation estimates by both methods. SOMNiBUS, a method for regional analysis, attempts to overcome some of these limitations. Currently, the most comprehensive assay for profiling DNA methylation is whole-genome bisulfite sequencing (WGBS), but its precision depends on read depth and it may be subject to sequencing errors. Abnormal DNA methylation is thought to contribute to the onset and progression of systemic sclerosis.
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