ArticleNucleic acids research2021
AtMAD: Arabidopsis thaliana multi-omics association database.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 36 citations in OpenAlex.
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- The circadian clock of Populus affects physiological, transcriptional and metabolomic responses to osmotic and ionic components of salt stress.Npj biological timing and sleep · 2025Article
- athisomiRDB: A comprehensive database of Arabidopsis isomiRs.Database : the journal of biological databases and curation · 2024Article
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- Crop-GPA: an integrated platform of crop gene-phenotype associations.NPJ systems biology and applications · 2024Article
- PRMD: an integrated database for plant RNA modifications.Nucleic acids research · 2024Article
- Genetic adaptations in the population history of Arabidopsis thaliana.G3 (Bethesda, Md.) · 2023Article
- IPOP: An Integrative Plant Multi-omics Platform for Cross-species Comparison and Evolutionary Study.Molecular biology and evolution · 2023Article
- Metabolome plasticity in 241 Arabidopsis thaliana accessions reveals evolutionary cold adaptation processes.Plant physiology · 2023Article
- Integration of eQTL and GWAS analysis uncovers a genetic regulation of natural ionomic variation in Arabidopsis.Plant cell reports · 2023Article
- A Comprehensive Gene Co-Expression Network Analysis Reveals a Role ofInternational journal of molecular sciences · 2022Article
- Feature importance network reveals novel functional relationships between biological features inFrontiers in plant science · 2022Article
- The 2021 Nucleic Acids Research database issue and the online molecular biology database collection.Nucleic acids research · 2021Article
- Biological Parts for Plant Biodesign to Enhance Land-Based Carbon Dioxide Removal.Biodesign research · 2021Review
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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 expression-methylation quantitative trait loci (emQTL), we identified 265 776 emQTLs and 122 344 pathway-mQTLs. For TWAS and EWAS, we obtained 62 754 significant phenotype-gene associations and 3 993 379 significant phenotype-methylation associations, respectively. Overall, the multi-omics associated network in AtMAD will provide new insights into exploring biological mechanisms of plants at multi-omics levels.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.