Identifying heterogeneous transgenerational DNA methylation sites via clustering in beta regression
Identifying heterogeneous transgenerational DNA methylation sites via clustering in beta regression
This paper explores the transgenerational DNA methylation pattern (DNA methylation transmitted from one generation to the next) via a clustering approach. Beta regression is employed to model the transmission pattern from parents to their offsprings at the population level. To facilitate this goal, an expectation maximization algorithm for parameter estimation along with a BIC criterion to determine the number of clusters is proposed. Applying our method to the DNA methylation data composed of 4063 CpG sites of 41 mother–father-infant triads, we identified a set of CpG sites in which DNA methylation transmission is dominated by fathers, while at a large number of CpG sites, DNA methylation is mainly maternally transmitted to the offspring.
2052-2072
Han, Shengtong
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Zhang, Hongmei
9f774048-54d6-4321-a252-3887b2c76db0
Lockett, Gabrielle A.
4d92a28c-f54c-431b-81f6-e82ad9057d7a
Mukherjee, Nandini
f64f02d6-2fd0-40db-88ee-5f85b59b8e0b
Holloway, John W.
4bbd77e6-c095-445d-a36b-a50a72f6fe1a
Karmaus, Wilfried
281d0e53-6b5d-4d38-9732-3981b07cd853
2015
Han, Shengtong
eee0c306-f700-4012-b9de-97b900034835
Zhang, Hongmei
9f774048-54d6-4321-a252-3887b2c76db0
Lockett, Gabrielle A.
4d92a28c-f54c-431b-81f6-e82ad9057d7a
Mukherjee, Nandini
f64f02d6-2fd0-40db-88ee-5f85b59b8e0b
Holloway, John W.
4bbd77e6-c095-445d-a36b-a50a72f6fe1a
Karmaus, Wilfried
281d0e53-6b5d-4d38-9732-3981b07cd853
Han, Shengtong, Zhang, Hongmei, Lockett, Gabrielle A., Mukherjee, Nandini, Holloway, John W. and Karmaus, Wilfried
(2015)
Identifying heterogeneous transgenerational DNA methylation sites via clustering in beta regression.
The Annals of Applied Statistics, 9 (4), .
(doi:10.1214/15-AOAS865).
Abstract
This paper explores the transgenerational DNA methylation pattern (DNA methylation transmitted from one generation to the next) via a clustering approach. Beta regression is employed to model the transmission pattern from parents to their offsprings at the population level. To facilitate this goal, an expectation maximization algorithm for parameter estimation along with a BIC criterion to determine the number of clusters is proposed. Applying our method to the DNA methylation data composed of 4063 CpG sites of 41 mother–father-infant triads, we identified a set of CpG sites in which DNA methylation transmission is dominated by fathers, while at a large number of CpG sites, DNA methylation is mainly maternally transmitted to the offspring.
Text
Han S Annal Appl Stat Identifying Heterogenous Transgenerational DNA Methylation Sites.pdf
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Accepted/In Press date: 5 August 2015
Published date: 2015
Organisations:
Human Development & Health
Identifiers
Local EPrints ID: 386607
URI: http://eprints.soton.ac.uk/id/eprint/386607
ISSN: 1932-6157
PURE UUID: a06e0cde-96f2-4b22-bc17-13f4bce54571
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Date deposited: 02 Feb 2016 12:32
Last modified: 15 Mar 2024 02:56
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Contributors
Author:
Shengtong Han
Author:
Hongmei Zhang
Author:
Gabrielle A. Lockett
Author:
Nandini Mukherjee
Author:
Wilfried Karmaus
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