FAQ
AtMAD is the first database to provide multi-level interactions between genome, transcriptome, methylome, environment, pathway and phenotype in Arabidopsis and allow researchers to identify variants, genes or methylations which are associated with specific phenotypes, environments and metabolic pathways. AtMAD describes and offers free access to substantially reliable associations among multi-omics of Arabidopsis, it integrates different data types altogether(genomics, transcriptomics, methylomics and phenomics) and provides dedicated tools to explore them.
Yes, all data in the AtMAD is public.
Yes, we provide download page in AtMAD database
cis-eQTL: eQTLs were defined if the SNP was within 1 Mb from the gene transcriptional start site (TSS)
trans-eQTL: eQTLs were defined if the SNP was beyond the region of 1 Mb from the gene transcriptional start site (TSS)
Environment-related eQTL: eQTLs that associated with at least one environmental factor
GWAS-related eQTL: eQTLs that related with known GWAS loci (collected from AraGWAS)
emQTL: emQTLs associated methylations and gene expression
Pathway-mQTL: Pathway-mQTLs connected methylations and pathways
Pathway-phenotype: Associations between pathways and phenotypes
GWAS: GWAS identified variant-trait associations. Phenotypes were collected from AraPheno, GWAS information was obtained from AraGWAS Catalog with bonferroni threshold
TWAS: TWAS identified associations between gene expression and phenotype
EWAS: EWAS identified associations between DNA methylation levels and phenotypes
| Data type | Details | Total numble of associations |
|---|---|---|
| cis-eQTL | eQTLs were defined if the SNP was within 1 Mb from the gene transcriptional start site (TSS) | 11,796 |
| trans-eQTL | eQTLs were defined if the SNP was beyond the region of 1 Mb from the gene transcriptional start site (TSS) | 10,119 |
| Environment-related eQTL | eQTLs that associated with at least one environmental factor | 68,837 |
| GWAS-related eQTL | eQTLs that related with known GWAS loci (collected from AraGWAS) | 149,622 |
| emQTL | emQTLs associated methylations and gene expression | 265,776 |
| Pathway-mQTL | Pathway-mQTLs connected methylations and pathways | 122,344 |
| Pathway-phenotype | Associations between pathways and phenotypes | 1,354 |
| GWAS | GWAS identified variant-trait associations. Phenotypes were collected from AraPheno, GWAS information was obtained from AraGWAS Catalog with bonferroni threshold | 44,636 |
| TWAS | TWAS identified associations between gene expression and phenotype | 62,754 |
| EWAS | EWAS identified associations between DNA methylation levels and phenotypes | 3,993,379 |
When clicking on the phenotype name you can get more detailed information about the phenotype, and a link to AraPheno is also provided, where you can download the phenotypic information.
When clicking on the pathway name you can get more detailed information about the pathway, and a link to AraCyc database is also provided.
Scientific Problems
We welcome any suggestions regarding how to improve our database, please feel free to contact us with feedback. Tieliu Shi: tieliushi@yahoo.com
Technical Problems
If you have any questions about the usage of AtMAD, please contact Jian Ouyang: ouyangjian12@163.com
DESeq2, Matrix eQTL, EIGENSOFT (7.2.1), GEMMA(0.98.1), PopLDdecay(3.41), python-scipy. All the parameters used here were described in AtMAD manuscript.