1) SNP-metabolite associations (mGWAS)
As of December 2021, 65 mGWAS papers had been found after searching PubMed, Web of
Science, bioRxiv, and medRxiv, after a thorough literature research. The summary statistics were
either collected from publicly available databases or supplementary data from the original
publications. Study-specific significant thresholds were used to pre-filter statistical associations
between metabolites and SNPs. Details of the curated mGWAS dataset can be found in our
Resources page: mGWAS-Explorer
3) LD proxy search
mGWAS-Explorer allow users to search for metabolites/diseases associations with proxies for
SNPs of interest using the HaploReg API or PhenoScanner API. The LD information is based on
the 1000 Genomes Project.
4) SNP-disease association
DisGeNET and OpenGWAS database were used to obtain SNP-disease associations. Particularly, DisGeNET contains both curated and literature data. The curated data include SNP-disease associations from UniProt, ClinVar, GWAS Catalog, and GWASdb. In contrast, OpenGWAS is a database of 244,868,980,310 genetic associations from 42,334 GWAS summary datasets.
Note, OpenGWAS is used to extract outcome GWAS in MR analysis.
5) Gene-metabolite association
Knowledge-based gene-metabolite association information was curated using KEGG, Recon3D,
and the Transporter Classification Database (TCDB).
7) Gene-disease association
DisGeNET was also used to obtain gene-disease associations.
8) Metabolite-disease association
HMDB was used to retrieve metabolite-disease associations.