engreitz
commented
2 months ago For the GWAS associations table, please update the columns and display to be similar to the OpenTargets version
For the eQTL table, update to have columns: • Gene • Biosample • Type (eQTL or sQTL) • Beta • P-value (in scientific notation, not log10 p-value) • Source (e.g. GTEx)
Could we put a summary of the different tables in the left-hand box, almost like a table of contents? This would give an easier way to see what types of information on the page, and it could also potentially report the number (e.g., 50 E-G predictions, 5 Coding Variant predictions, etc.) as a summary of what the variant is doing? Alternatively, rather than a table of contents, we could add a text summary of the key info from the page. I will need to think more about exactly how that should look, but something like the top of the OpenTargets Genetics variant table
Variants in LD table: Default to show 10 entries instead of 50. Sort by r^2 rather than D'. Include the variant itself in the table as well (with the rsID bolded to distinguish it from others)
Downloading data as CSVs: Relevant to multiple tables — it doesn't seem like the downloadable CSVs have all of the same columns or column names as that shown in the portal. e.g. the "Variants in LD" table doesn't have rsid. The "Variant Phenotypes" table doesn't have all of the same columns, and the columns are named differently. Would be nice if the CSVs can exactly match the content shown on the page in columns, column names, and order
Phenotype table: We could shorten the list of columns and reformat to match the OpenTargets version:
"Variant Phenotypes" heading should be "GWAS Associations" instead. Subtitle text: "Which phenotypes are associated with this variant through genome-wide association studies?"
"Coding Variants" heading should be "Coding Variant Predictions". Subtitle text: "What are the predicted impacts of this variant on protein function?"
What is the "Genes" table at the bottom? Is it QTL information? Then title shoudl be "QTL associations", subtitle "Is this variant an eQTL or spliceQTL?" Also, the organization of this section is confusing to me. I'm not sure what is shown when you click the variant arrow to drop down the menu. I would prefer if the table were merged into one instead of having two separate tables linked by horizontal lines. What is the source of this data? I could help write a subtitle to explain if more info is provided