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Combinatorial ident...
Combinatorial identification of DNA methylation patterns over age in the human brain
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- Torabi Moghadam, Behrooz (författare)
- Uppsala universitet,Beräkningsbiologi och bioinformatik
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- Dabrowski, Michal (författare)
- Polish Acad Sci, Nencki Inst Expt Biol, Lab Bioinformat, Neurobiol Ctr, Warsaw, Poland.
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- Kaminska, Bozena (författare)
- Polish Acad Sci, Nencki Inst Expt Biol, Lab Bioinformat, Lab Mol Neurobiol, Warsaw, Poland.
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- Grabherr, Manfred G. (författare)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi
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- Komorowski, Jan (författare)
- Uppsala universitet,Beräkningsbiologi och bioinformatik,Polish Acad Sci, Inst Comp Sci, PL-01248 Warsaw, Poland.
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(creator_code:org_t)
- 2016-09-23
- 2016
- Engelska.
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Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 17
- Relaterad länk:
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https://uu.diva-port... (primary) (Raw object)
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https://bmcbioinform...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- Background: DNA methylation plays a key role in developmental processes, which is reflected in changing methylation patterns at specific CpG sites over the lifetime of an individual. The underlying mechanisms are complex and possibly affect multiple genes or entire pathways. Results: We applied a multivariate approach to identify combinations of CpG sites that undergo modifications when transitioning between developmental stages. Monte Carlo feature selection produced a list of ranked and statistically significant CpG sites, while rule-based models allowed for identifying particular methylation changes in these sites. Our rule-based classifier reports combinations of CpG sites, together with changes in their methylation status in the form of easy-to-read IF-THEN rules, which allows for identification of the genes associated with the underlying sites. Conclusion: We utilized machine learning and statistical methods to discretize decision class (age) values to get a general pattern of methylation changes over the lifespan. The CpG sites present in the significant rules were annotated to genes involved in brain formation, general development, as well as genes linked to cancer and Alzheimer's disease.
Ämnesord
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinsk bioteknologi -- Medicinsk bioteknologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Medical Biotechnology -- Medical Biotechnology (hsv//eng)
Nyckelord
- DNA methylation
- Aging
- Rule-based classification
- Feature selection
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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