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eRNA_QTL_website.pptx
- 1. Web portal for eRNA-QTLs A step-by-step guide
- 2. Data and methods • Data were obtained from the Genotype-Tissue Expression (GTEx), including 838 donors, 54 tissues, and two cell lines. Genotype data from whole-genome sequencing (WGS) was sequenced on an Illumina HiSeq 2000. • To test for eRNA-QTLs, we first used the permutation pass with 1000 permutations recommended to characterize the null distribution of associations for each eRNA separately and obtained a 5% false discovery rate for multiple testing applied in R using qvalue. Second, a nominal pass was performed. Nominal p-values for all SNP-eRNA pairs within the cis-window (1Mbp) were obtained with the nominal pass implemented in the QTLtools package. Both permutation and nominal pass were applied the QTLtools-implemented “--normal” option to rank normal transform the phenotype quantifications. SNP-eRNA associations reaching the significance threshold corresponding to FDR < 0.05 were retained to further analysis. The eRNA expression matrix was also normalized using the “--normal” option. Linear regression analysis was performed between SNPs and all eRNAs outside their cis windows (1Mbp), accounting for the covariates previously mentioned.
- 3. Part 1: Querying eRNA-QTLs of interest Part 2: Genome Browser Part 3: Visualization of GWAS and eRNA-QTLs colocalization events Part 4: Disease/trait-associated eRNA-QTLs Part 5: Downloading data of eRNA-QTLs
- 4. Step 2: Select tissue type of interest (e.g. Adipose_Subcutaneous) Part 1 Querying eRNA-QTLs of interest Step 1: Quick search by eRNA or rs ID (e.g. ENSR00000069687 or rs4467826)
- 5. Step 3: Search a rsid ( e.g. rs9323457)
- 6. Step 4: Relevant eRNA-QTLs will automatically show
- 7. Part 2 Genome Browser Step 1: Click “Genome Browser” in navigation bar. This process might consume some time to load the frame. Thank you for waiting.
- 8. IGV.js was used to construct the frame of genome browser Based on the hg38 genome Download SVG Search by genome position (e.g. chr14:64423444-65063275).
- 9. Mouse click to see detailed information Mouse click to config tracks Part 2 Genome Browser
- 10. Part 3 Visualization of GWAS and eRNA-QTLs colocalization events Step 1: Click to load example data Quick guide
- 11. Part 3 Visualization of GWAS and eRNA-QTLs colocalization events Step 2: Click to plot Step 3: Download PDF file
- 12. Part 4: Disease/trait-associated eRNA-QTLs Step 1:Search a disease/trait type (e.g. Telomere length) Step 2: Select a tissue(e.g. Adipose Subcutaneous) This process might consume some time to search the data or scroll to the next page due to the large data. Thank you for waiting.
- 13. Part 5 Downloading data of eRNA QTLs Step 1: Click “Downloads” h
- 14. Step 2: Click any file name for Visualizing and Downloading Download file: