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cis-eQTL：Expression quantitative trait loci (eQTLs) are genomic loci that explain variation in expression levels of mRNAs. eQTLs located near the gene-of-origin (gene which produces the transcript or protein) are referred to as local eQTLs or cis-eQTLs. Here, eQTLs were defined if the SNP was within 1 Mb from the gene transcriptional start site (TSS).
| SNP | Alleles | Alteration number | Gene | Beta | tstat | Pvalue | FDR | Display |
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trans-eQTL: Chromosomal loci that explain variance in expression traits are called eQTLs, those located distant from their gene of origin, often on different chromosomes, are referred to as distant eQTLs or trans-eQTLs. Here, eQTLs were defined if the SNP was beyond the region of 1 Mb from the gene transcriptional start site (TSS).
| SNP | Alleles | Alteration number | Gene | Beta | tstat | Pvalue | FDR | Display |
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Environment-related eQTL: eQTLs that associated with at least one environmental factor. Environmental factors contained longitude, latitude, elevation and 19 standard WorldClim Bioclimatic variables. BIO1 = Annual Mean Temperature, BIO2 = Mean Diurnal Range (Mean of monthly (max temp - min temp)), BIO3 = Isothermality (BIO2/BIO7) (×100), BIO4 = Temperature Seasonality (standard deviation ×100), BIO5 = Max Temperature of Warmest Month, BIO6 = Min Temperature of Coldest Month, BIO7 = Temperature Annual Range (BIO5-BIO6), BIO8 = Mean Temperature of Wettest Quarter, BIO9 = Mean Temperature of Driest Quarter, BIO10 = Mean Temperature of Warmest Quarter, BIO11 = Mean Temperature of Coldest Quarter, BIO12 = Annual Precipitation, BIO13 = Precipitation of Wettest Month, BIO14 = Precipitation of Driest Month, BIO15 = Precipitation Seasonality (Coefficient of Variation), BIO16 = Precipitation of Wettest Quarter, BIO17 = Precipitation of Driest Quarter, BIO18 = Precipitation of Warmest Quarter, BIO19 = Precipitation of Coldest Quarter.
| eQTL | Alleles | Alteration | Environment | Beta | Pvalue | FDR | Type | Display |
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GWAS-related eQTL: eQTLs that related with known GWAS loci (collected from AraGWAS (2020-1)). Here, eQTLs that overlap with GWAS tagSNPs and LD SNPs (LD-r2 ≥ 0.5) were identified as GWAS-related eQTLs.
| eQTL loci | eQTL alleles | eQTL alteration | GWAS loci | GWAS alleles | GWAS alteration | LD | GWAS phenotype | Phenotype Ontology | Type |
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GWAS: GWAS is an observational study of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait. GWAS identified variant-trait associations. Here, Phenotypes were collected from AraPheno (2020-1), GWAS information was obtained from AraGWAS Catalog (2020-1) with bonferroni threshold.
| SNP | Chr | Position | Score,(-log10(p-value)) | MAF | Study | Phenotype | Phenotype Ontology | Reference | Alteration | Genename | Function | Impact | Effect |
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TWAS: TWAS identified associations between gene expression and phenotype. Phenotypes were collected from AraPheno (2020-1).
| Phenotype | Phenotype Ontology | Gene | Pearson | Pvalue_Pearson | FDR_Pearson | Spearman | Pvalue_Spearman | FDR_Spearman | Study | Display |
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EWAS: EWAS identified associations between DNA methylation level and phenotype. Phenotypes were collected from AraPheno (2020-1).
| Phenotype | Phenotype Ontology | Methylation | Pearson | Pvalue_Pearson | FDR_Pearson | Spearman | Pvalue_Spearman | FDR_Spearman | Study | Display |
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Pathway-mQTL: Pathway-mQTLs connected methylations and pathways, Pathway activities were calculated with DESeq2 normalized read count for each pathway from the latest
AraCyc15.0(Arabidopsis thaliana col).
| Pathway | Methylation | Pearson | Pvalue_Pearson | FDR_Pearson | Spearman | Pvalue_Spearman | FDR_Spearman |
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Phenotype-pathway: Associations between pathways and phenotypes. Pathway activities were calculated with DESeq2 normalized read count for each pathway from the latest AraCyc15.0(Arabidopsis thaliana col), and Phenotypes were collected from AraPheno(2020-1).
| Phenotype | Phenotype Ontology | Pathway | Pearson | Pvalue_Pearson | FDR_Pearson | Spearman | Pvalue_Spearman | FDR_Spearman | Study |
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emQTL：emQTL calculated correlation between methylation level and gene expression. It reveals potential methylation sites that can affect gene expression.
| Gene | Methylation | Pearson | Pvalue | FDR |
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Browse Browse by Gene
| Gene ID | Gene name | Protein-protein interaction | Mutant | cis-eQTL | trans-eQTL | Pathway | TWAS | emQTL |
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