{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,18]],"date-time":"2026-01-18T02:58:41Z","timestamp":1768705121466,"version":"3.49.0"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2020,11,21]],"date-time":"2020-11-21T00:00:00Z","timestamp":1605916800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31671377"],"award-info":[{"award-number":["31671377"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31872139"],"award-info":[{"award-number":["31872139"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31171264"],"award-info":[{"award-number":["31171264"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Municipal Science and Technology","award":["2017SHZDZX01"],"award-info":[{"award-number":["2017SHZDZX01"]}]},{"name":"Beihang University & Capital Medical University Plan","award":["BHME-201901"],"award-info":[{"award-number":["BHME-201901"]}]},{"name":"Beihang University & Capital Medical University Plan","award":["BHME-201904"],"award-info":[{"award-number":["BHME-201904"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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\u2013methylation 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.<\/jats:p>","DOI":"10.1093\/nar\/gkaa1042","type":"journal-article","created":{"date-parts":[[2020,10,21]],"date-time":"2020-10-21T11:22:39Z","timestamp":1603279359000},"page":"D1445-D1451","source":"Crossref","is-referenced-by-count":32,"title":["AtMAD: <i>Arabidopsis thaliana<\/i> multi-omics association database"],"prefix":"10.1093","volume":"49","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9564-9985","authenticated-orcid":false,"given":"Yiheng","family":"Lan","sequence":"first","affiliation":[{"name":"Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, Heilongjiang 150040, China"},{"name":"The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China"}]},{"given":"Ruikun","family":"Sun","sequence":"additional","affiliation":[{"name":"The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China"}]},{"given":"Jian","family":"Ouyang","sequence":"additional","affiliation":[{"name":"The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China"}]},{"given":"Wubing","family":"Ding","sequence":"additional","affiliation":[{"name":"The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China"}]},{"given":"Min-Jun","family":"Kim","sequence":"additional","affiliation":[{"name":"Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, Heilongjiang 150040, China"}]},{"given":"Jun","family":"Wu","sequence":"additional","affiliation":[{"name":"The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China"}]},{"given":"Yuhua","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, Heilongjiang 150040, China"}]},{"given":"Tieliu","family":"Shi","sequence":"additional","affiliation":[{"name":"The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China"},{"name":"Big Data and Engineering Research Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China"}]}],"member":"286","published-online":{"date-parts":[[2020,11,21]]},"reference":[{"key":"2021010313123280200_B1","doi-asserted-by":"crossref","first-page":"D1060","DOI":"10.1093\/nar\/gkw1029","article-title":"AtPID: a genome-scale resource for genotype-phenotype associations in Arabidopsis","volume":"45","author":"Lv","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2021010313123280200_B2","doi-asserted-by":"crossref","first-page":"D1150","DOI":"10.1093\/nar\/gkx954","article-title":"The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog","volume":"46","author":"Togninalli","year":"2018","journal-title":"Nucleic Acids 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