MesaEpiGenomics

The MESA Epigenomics and Transcriptomics Study was funded by a National Heart, Lung and Blood Institute grant (R01HL101250) through the NIH Roadmap Epigenomics Program in 2009. Leveraging MESA exam 5 (2010-2012), we purified fresh monocytes and CD4+ T cells from 2,600 MESA participants (Caucasian, African American, and Hispanic men and women aged 55 - 94 years) across the four MESA field centers (Forsyth County, NC; Baltimore, MD; New York, NY; and St. Paul, MN). Our ongoing global gene expression and DNA methylation studies uses the Illumina microarray, RNAseq, and miRNAseq technologies. The rich MESA database will enable the epigenomic and transcriptomic study of the genetic, physiological, environmental and clinical characteristics of the MESA population.

expression-associated Methylation Site (eMS) Database

A project has been launched to investigate potential gene expression regulatory methylation sites in humans by examining the association between CpG methylation and gene expression in purified human monocytes from a large study population (1,264 community-dwelling participants in the Multi-Ethnic Study of Atherosclerosis (MESA)). The Illumina HumanHT-12 v4 Expression BeadChip and the Illumina HumanMethylation450 BeadChip were used to provide genome-wide coverage of mRNA expression and DNA methylation, respectively. This data enabled us to identify 11,203 potential cis-acting CpG loci whose degree of methylation was associated with gene expression (eMS) at a False Discovery Rate (FDR) threshold of 0.001.

eMS FlowChart MesaEpiGenomics 

 

eMS Database Details

The eMS Database is used to store the methylation-gene expression association results from 11,203 CpG sites with expression-associated methylation, and to enable a convenient search for genes and eMS. Particularly, we focus on cis-acting genetic regulation, defined as associations between CpG methylation sites within 1 MB of expressed transcripts (from the transcription start site). Each of these associations were performed using a linear regression model adjusted for age, sex, ethnicity, study site, expression/methylation chip, methylation position (for age-CpG methylation analyses only), and residual sample contamination with non-targeted cells (see publication for methods). The primary outcome was gene expression levels, and the main predictor was CpG methylation levels.

Citing MESA EpiGenomics Resources

When using data from the eMS Database in a research work that will be published in a journal or on the internet, please cite the following publication: Methylomics of Gene Expression in Human Monocytes Yongmei Liu; Jingzhong Ding; Lindsay M. Reynolds; Kurt Lohman; Thomas C. Register; Alberto de la Fuente; Timothy D. Howard; Greg A. Hawkins; Wei Cui; Jessica Morris; Shelly G. Smith; R. Graham Barr; Joel D. Kaufman; Gregory L. Burke; Wendy Post; Steven Shea; Charles E. McCall; David Siscovick; David R. Jacobs Jr; Russell P. Tracy; David M. Herrington; Ina Hoeschele; Hum Mol Genet 22 (24), 5065-5074 (2013)

Query the MESA EpiGenomics eMS Database: 

Download the MESA EpiGenomics eMS Database (xls):

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