ArticleJCO clinical cancer informatics2020
Epigenetic Conservation Is a Beacon of Function: An Analysis Using Methcon5 Software for Studying Gene Methylation.
Article in JCO clinical cancer informatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed, 5 citations in OpenAlex.
- Informatics at the Frontier of Cancer Research.Cancer research · 2025Review
- A Bayesian hierarchical model to estimate DNA methylation conservation in colorectal tumors.Bioinformatics (Oxford, England) · 2021Article
- Article
- Informatics Tools for Cancer Research and Care: Bridging the Gap Between Innovation and Implementation.JCO clinical cancer informatics · 2020Article
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Authors and funding
5 authors at 1 institution in 1 country.
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Abstract
purposeDifferent epigenetic configurations allow one genome to develop into multiple cell types. Although the rules governing what epigenetic features confer gene expression are increasingly being understood, much remains uncertain. Here, we used a novel software package, Methcon5, to explore whether the principle of biologic conservation can be used to identify expressed genes. The hypothesis is that epigenetic configurations of important expressed genes will be conserved within a tissue. MATERIALS AND
methodsWe compared the DNA methylation of approximately 850,000 CpG sites between multiple clonal crypts or glands of human colon, small intestine, and endometrium. We performed this analysis using the new software package, Methcon5, which enables detection of regions of high (or low) conservation.
resultsWe showed that DNA methylation is preferentially conserved at gene-associated CpG sites, particularly in gene promoters (eg, near the transcription start site) or the first exon. Furthermore, higher conservation correlated well with gene expression levels and performed better than promoter DNA methylation levels. Most conserved genes are in canonical housekeeping pathways.
conclusionThis study introduces the new software package, Methcon5. In this example application, we showed that epigenetic conservation provides an alternative method for identifying functional genomic regions in human tissues.
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