AtMAD: Arabidopsis thaliana multi-omics association database.

Nucleic Acids Research
Yiheng LanTieliu Shi

Abstract

Integration analysis of multi-omics data provides a comprehensive landscape for understanding biological systems and mechanisms. The abundance of high-quality multi-omics data (genomics, transcriptomics, methylomics and phenomics) for the model organism Arabidopsis thaliana enables scientists to study the genetic mechanism of many biological processes. However, no resource is available to provide comprehensive and systematic multi-omics associations for Arabidopsis. Here, we developed an Arabidopsis thaliana Multi-omics Association Database (AtMAD, http://www.megabionet.org/atmad), a public repository for large-scale measurements of associations between genome, transcriptome, methylome, pathway and phenotype in Arabidopsis, designed for facilitating identification of eQTL, emQTL, Pathway-mQTL, Phenotype-pathway, GWAS, TWAS and EWAS. Candidate variants/methylations/genes were identified in AtMAD for specific phenotypes or biological processes, many of them are supported by experimental evidence. Based on the multi-omics association strategy, we have identified 11 796 cis-eQTLs and 10 119 trans-eQTLs. Among them, 68 837 environment-eQTL associations and 149 622 GWAS-eQTL associations were identified and stored in AtMAD. For expre...Continue Reading

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Datasets Mentioned

BETA
GSE80744
GSE43857

Methods Mentioned

BETA
RNA-seq
genotyping
MethylC-seq
gene-knockout

Software Mentioned

AraGWAS
EIGENSOFT
AraPheno
WorldClim
MySQL
smartpca
AraGWAS Catalog
AtMAD
GEMMA
PopLDdecay

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