Gene-methylation epistatic analyses via the W-test identifies enriched signals of neuronal genes in patients undergoing lipid-control treatment
Abstract An increasing number of studies are focused on the epigenetic regulation of DNA to affect gene expression without modifications to the DNA sequence. Methylation plays an important role in shaping disease traits; however, previous studies were mainly experiment, based, resulting in few repor...
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doaj-9f0f7ad94b234d228d700747eabf2bf52020-11-24T20:53:50ZengBMCBMC Proceedings1753-65612018-09-0112S918719210.1186/s12919-018-0143-8Gene-methylation epistatic analyses via the W-test identifies enriched signals of neuronal genes in patients undergoing lipid-control treatmentRui Sun0Haoyi Weng1Ruoting Men2Xiaoxuan Xia3Ka Chun Chong4William K. K. Wu5Benny Chung-Ying Zee6Maggie Haitian Wang7Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, the Chinese University of Hong KongDivision of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, the Chinese University of Hong KongDivision of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, the Chinese University of Hong KongDivision of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, the Chinese University of Hong KongDivision of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, the Chinese University of Hong KongDepartment of Anaesthesia and Intensive Care, the Chinese University of Hong KongDivision of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, the Chinese University of Hong KongDivision of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, the Chinese University of Hong KongAbstract An increasing number of studies are focused on the epigenetic regulation of DNA to affect gene expression without modifications to the DNA sequence. Methylation plays an important role in shaping disease traits; however, previous studies were mainly experiment, based, resulting in few reports that measured gene–methylation interaction effects via statistical means. In this study, we applied the data set adaptive W-test to measure gene–methylation interactions. Performance was evaluated by the ability to detect a given set of causal markers in the data set obtained from the GAW20. Results from simulation data analyses showed that the W-test was able to detect most markers. The method was also applied to chromosome 11 of the experimental data set and identified clusters of genes with neuronal and retinal functions, including MPPED2I, GUCY2E, NAV2, and ZBTB16. Genes from the TRIM family were also identified; these genes are potentially related to the regulation of triglyceride levels. Our results suggest that the W-test could be an efficient and effective method to detect gene–methylation interactions. Furthermore, the identified genes suggest an interesting relationship between lipid levels and the etiology of neurological disorders.http://link.springer.com/article/10.1186/s12919-018-0143-8 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Rui Sun Haoyi Weng Ruoting Men Xiaoxuan Xia Ka Chun Chong William K. K. Wu Benny Chung-Ying Zee Maggie Haitian Wang |
spellingShingle |
Rui Sun Haoyi Weng Ruoting Men Xiaoxuan Xia Ka Chun Chong William K. K. Wu Benny Chung-Ying Zee Maggie Haitian Wang Gene-methylation epistatic analyses via the W-test identifies enriched signals of neuronal genes in patients undergoing lipid-control treatment BMC Proceedings |
author_facet |
Rui Sun Haoyi Weng Ruoting Men Xiaoxuan Xia Ka Chun Chong William K. K. Wu Benny Chung-Ying Zee Maggie Haitian Wang |
author_sort |
Rui Sun |
title |
Gene-methylation epistatic analyses via the W-test identifies enriched signals of neuronal genes in patients undergoing lipid-control treatment |
title_short |
Gene-methylation epistatic analyses via the W-test identifies enriched signals of neuronal genes in patients undergoing lipid-control treatment |
title_full |
Gene-methylation epistatic analyses via the W-test identifies enriched signals of neuronal genes in patients undergoing lipid-control treatment |
title_fullStr |
Gene-methylation epistatic analyses via the W-test identifies enriched signals of neuronal genes in patients undergoing lipid-control treatment |
title_full_unstemmed |
Gene-methylation epistatic analyses via the W-test identifies enriched signals of neuronal genes in patients undergoing lipid-control treatment |
title_sort |
gene-methylation epistatic analyses via the w-test identifies enriched signals of neuronal genes in patients undergoing lipid-control treatment |
publisher |
BMC |
series |
BMC Proceedings |
issn |
1753-6561 |
publishDate |
2018-09-01 |
description |
Abstract An increasing number of studies are focused on the epigenetic regulation of DNA to affect gene expression without modifications to the DNA sequence. Methylation plays an important role in shaping disease traits; however, previous studies were mainly experiment, based, resulting in few reports that measured gene–methylation interaction effects via statistical means. In this study, we applied the data set adaptive W-test to measure gene–methylation interactions. Performance was evaluated by the ability to detect a given set of causal markers in the data set obtained from the GAW20. Results from simulation data analyses showed that the W-test was able to detect most markers. The method was also applied to chromosome 11 of the experimental data set and identified clusters of genes with neuronal and retinal functions, including MPPED2I, GUCY2E, NAV2, and ZBTB16. Genes from the TRIM family were also identified; these genes are potentially related to the regulation of triglyceride levels. Our results suggest that the W-test could be an efficient and effective method to detect gene–methylation interactions. Furthermore, the identified genes suggest an interesting relationship between lipid levels and the etiology of neurological disorders. |
url |
http://link.springer.com/article/10.1186/s12919-018-0143-8 |
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