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A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control

Yinming Jiao, Martin Widschwendter, Andrew E. Teschendorff
2014 Bioinformatics  
The algorithm identifies gene modules of coordinated differential methylation and differential expression in the context of a human interactome.  ...  Results: Here, we present a novel functional supervised algorithm, called Functional Epigenetic Modules (FEM), for the integrative analysis of Infinium 450k DNA methylation and matched or unmatched gene  ...  Similarly, FEM could be applied to cellular differentiation data to identify cell type-specific gene expression modules under the regulation of DNA methylation.  ... 
doi:10.1093/bioinformatics/btu316 pmid:24794928 fatcat:wxqwwave3rh2fnn24ipskyemvu

Integration of gene expression and DNA methylation identifies epigenetically controlled modules related to PM2.5 exposure

Simon Kebede Merid, Mariona Bustamante, Marie Standl, Jordi Sunyer, Joachim Heinrich, Nathanaël Lemonnier, Daniel Aguilar, Josep Maria Antó, Jean Bousquet, Loreto Santa-Marina, Aitana Lertxundi, Anna Bergström (+5 others)
2021 Environment International  
Further, by integrating gene expression with DNA methylation using Functional Epigenetic Modules algorithms, we identified 9 and 6 modules in relation to PM2.5 exposure at birth and at current address,  ...  Importantly, we identified several significant interactome hotspots of gene modules of relevance for complex diseases in relation to PM2.5 exposure.  ...  We additionally acknowledge Alexandra Ek, Sandra Ekström, André Lauber and Niklas Andersson for excellent data management.  ... 
doi:10.1016/j.envint.2020.106248 pmid:33212358 fatcat:6bgrpjyievcgdh25pnlz5pe6su

Transcriptional Associations of Osteoarthritis-Mediated Loss of Epigenetic Control in Articular Cartilage

Wouter den Hollander, Yolande F. M. Ramos, Nils Bomer, Stefan Elzinga, Ruud van der Breggen, Nico Lakenberg, Wesley J. de Dijcker, H. Eka D. Suchiman, Bouke J. Duijnisveld, Jeanine J. Houwing-Duistermaat, P. Eline Slagboom, Steffan D. Bos (+2 others)
2015 Arthritis & Rheumatology  
Transcriptional activity of CpG was assessed using gene expression data and DNA methylation data for preserved and lesional articular cartilage samples.  ...  Finally, we observed 31 and 26 genes for which methylation and expression, respectively, were additionally affected by genetic variation. Conclusion.  ...  Mr. den Hollander had full access to all of the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis. Study conception and design.  ... 
doi:10.1002/art.39162 pmid:25892573 fatcat:k6zt7no5mbaq7jtw4q2l5w34gy

Applications of integrative OMICs approaches to gene regulation studies

Jing Qin, Bin Yan, Yaohua Hu, Panwen Wang, Junwen Wang
2016 Quantitative Biology  
Integrating multi-dimensional OMICs data will generate novel insights into system-level gene regulations and serves as a foundation for further hypothesis-driven research.  ...  Functional genomics employs dozens of OMICs technologies to explore the functions of DNA, RNA and protein regulators in gene regulation processes.  ...  ACKNOWLEDGEMENTS COMPLIANCE WITH ETHICS GUIDELINES The authors Jing Qin, Bin Yan, Yaohua Hu, Panwen Wang and Junwen Wang declare that they have no conflict of interests.  ... 
doi:10.1007/s40484-016-0085-y fatcat:z5ei3ztspne2lmczdca4w4z4za

PD_NGSAtlas: a reference database combining next-generation sequencing epigenomic and transcriptomic data for psychiatric disorders

Zheng Zhao, Yongsheng Li, Hong Chen, Jianping Lu, Peter M Thompson, Juan Chen, Zishan Wang, Juan Xu, Chun Xu, Xia Li
2014 BMC Medical Genomics  
In addition to these data that were generated in-house, we have included, and will continue to include, published DNA methylation and gene expression data from other research groups, with a focus on psychiatric  ...  A genome browser has been developed to provide integrative and detailed views of multidimensional data in a given genomic context, which can help researchers understand molecular mechanisms from epigenetic  ...  The module for the identification of differentially expressed genes (DEGs) is realised by R and Perl script.  ... 
doi:10.1186/s12920-014-0071-z pmid:25551368 pmcid:PMC4308070 fatcat:kkd3k4sfnbg2zexdc5ivztx2im

Systems biology approaches to epidemiological studies of complex diseases

Hongzhe Li
2013 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
I focus my review on integrative approaches for genome-wide genetic variants and gene expression data, methods for joint analysis of genetic and epigenetic variants and methods for analysis of microbiome  ...  Statistical methods such as mediation analysis, high dimensional instrumental variable regression, sparse signal recovery and compositional data regression provide potential frameworks for integrative  ...  Wei Lin and Sihai Dave Zhao for helpful discussions. The research was supported by NIH grants CA127334 and GM097505.  ... 
doi:10.1002/wsbm.1242 pmid:24019288 pmcid:PMC3947451 fatcat:vjqy2igosbcmla5gxxn4n4sgn4

EpiMOLAS: an intuitive web-based framework for genome-wide DNA methylation analysis

Sheng-Yao Su, I-Hsuan Lu, Wen-Chih Cheng, Wei-Chun Chung, Pao-Yang Chen, Jan-Ming Ho, Shu-Hwa Chen, Chung-Yen Lin
2020 BMC Genomics  
To our knowledge, the EpiMOLAS framework, consisting of DocMethyl and EpiMOLAS_web, is the first approach to include containerization technology and a web-based system for WGBS data analysis from raw data  ...  First, we set up the required tools in Galaxy and developed workflows to calculate the methylation level from raw WGBS data and generate a methylation status summary, the mtable.  ...  Acknowledgments The authors thank anonymous reviewers for providing comments and suggestions that helped us improve quality and clarity of the manuscript.  ... 
doi:10.1186/s12864-019-6404-8 pmid:32241255 fatcat:bpagtry47bez5jr2i537jzyhpe


Myriam Fornage, Hieab H.H. Adams, Joshua C. Bis, Eric Boerwinkle, Ian J. Deary, Hans J. Grabe, Lifang Hou, M. Arfan Ikram, Min A. Jhun, Lenore J. Launer, Michelle Luciano, Sudha Seshadri (+4 others)
2018 Alzheimer's & Dementia  
types, 2) differential expression gene sets from these data, and 3) network topological summaries for 42 AD associated modules from these data.  ...  Conclusions: We provide a framework for assessment and integration of systems biology outputs from the AMP-AD consortia.  ...  Analyses included 1,111 Caucasian participants with whole blood expression data on 11,376 genes (imputed from genome-wide genotyping using Pre-diXcan), 1,097 fasting plasma metabolites, and up to 19 AD  ... 
doi:10.1016/j.jalz.2018.06.2784 fatcat:2hwq5tpcuja6bizdrm5ivzyw3e

Bioinformatics challenges and perspectives when studying the effect of epigenetic modifications on alternative splicing

Clare Pacini, Magdalena J. Koziol
2018 Philosophical Transactions of the Royal Society of London. Biological Sciences  
These models can be used to identify alternative splicing and epigenetic changes across different phenotypes.  ...  Here, we give a brief overview of the role of epigenetics in alternative splicing and disease.  ...  The authors are grateful to John Gurdon, Charles Bradshaw and Jerome Jullien for reading the manuscript, useful comments and discussions on the topic.  ... 
doi:10.1098/rstb.2017.0073 pmid:29685977 pmcid:PMC5915717 fatcat:nkiaoku5rjhivdgbaurwrlqzm4

Systems genomics analysis centered on epigenetic inheritance supports development of a unified theory of biology

A. Sharma
2015 Journal of Experimental Biology  
This article provides a proof of concept for evolutionary transgenerational systems biology, proposed recently in the context of epigenetic inheritance in mammals.  ...  Gene set enrichment analysis of available genome-level mammalian data presented here seem consistent with the concept that: (1) heritable information about environmental effects in somatic cells is communicated  ...  For example, a recent study has revealed that several thousand genes escape genome-wide DNA demethylation in human PGCs .  ... 
doi:10.1242/jeb.125922 pmid:26347561 fatcat:7ahqn6lo6resrl4kdstvtfvqxi

Epigenetics studies of fetal alcohol spectrum disorder: where are we now?

Alexandre A Lussier, Joanne Weinberg, Michael S Kobor
2017 Epigenomics  
Acknowledgements The authors thank NeuroDevNet for continuous encouragement and support for this work. They would also like to thank  ...  of DNA to modulate gene expression and cellular functions without changes to underlying genomic sequences [28] .  ...  DNA methylation can also directly control the binding of transcription factors and repressors to gene regulatory regions, such as promoters and enhancers, to modulate gene expression patterns [41] .  ... 
doi:10.2217/epi-2016-0163 pmid:28234026 pmcid:PMC5549650 fatcat:3eaiahxemvhm7mmuu67mmrh324

Global DNA Methylation Remodeling Accompanies CD8 T Cell Effector Function

C. D. Scharer, B. G. Barwick, B. A. Youngblood, R. Ahmed, J. M. Boss
2013 Journal of Immunology  
Acknowledgments We thank members of the Boss and Ahmed laboratories for helpful comments and critiques, as well as the Southern California Genotyping Consortium for sequencing and the Emory University  ...  Flow Core for cell isolation.  ...  To derive an understanding of the epigenetic mechanisms controlling this differentiation, we mapped genome-wide DNA methylation in naive and day 8 (D8) effector CD8 T cells following LCMV Armstrong infection  ... 
doi:10.4049/jimmunol.1301395 pmid:23956425 pmcid:PMC3800465 fatcat:m4zc5orrubcohcpqtvxqgihlje

The role of genomic vs. epigenomic variation in shaping patterns of convergent transcriptomic variation across continents in a young species complex [article]

Clement Rougeux, Martin Laporte, Pierre-Alexandre Gagnaire, Louis Bernatchez
2019 bioRxiv   pre-print
We first found evidence for 149 convergent differentially methylated regions (DMRs) between species across continents, which significantly influenced levels of gene expression.  ...  This study provides a rare qualitative and quantitative documentation of the relative role of genomic, DNA methylation and their interaction in shaping patterns of convergent gene expression during the  ...  L.B also holds the Canadian Research Chair in genomics and conservation of aquatic resources, which funded the research infrastructure for this project.  ... 
doi:10.1101/784231 fatcat:4wp6bjfjebetrc3o7v7dc62boa

Integrating Epigenomics into the Understanding of Biomedical Insight

Yixing Han, Ximiao He
2016 Bioinformatics and Biology Insights  
A comprehensive understanding of epigenetic mechanisms, their interactions, and alterations in health and diseases genome widely has become a priority in biological research.  ...  In this review, we introduce the epigenetics pioneering achievements in health status and complex diseases; next, we give a systematic review of the epigenomics data generation, summarize public resources  ...  A common interest is to inspect or compare the DNA methylation and histone modification levels in a selected genomic region, such as gene locus, regulatory regions by a genome browser, either a Web-based  ... 
doi:10.4137/bbi.s38427 pmid:27980397 pmcid:PMC5138066 fatcat:ne6mu3bdhzhzno5hqjvgmxp3nu

Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response

Rohini Garg, VVS Narayana Chevala, Rama Shankar, Mukesh Jain
2015 Scientific Reports  
Numerous differentially methylated regions (DMRs) among different cultivars were identified and many of which were associated with differential expression of genes important for abiotic stress response  ...  DNA methylation has been proposed as one of the major factors that can modulate gene expression.  ...  Scott Jackson, University of Georgia, for helpful suggestions.  ... 
doi:10.1038/srep14922 pmid:26449881 pmcid:PMC4598828 fatcat:alikv53vo5dhjojdd5jf5oh5t4
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