JOB: Japan Omics Browser provides integrative visualization of multi-omics data

Area of Science:

• Genomics
• Bioinformatics
• Human Genetics

Background:

• Understanding human gene regulation is crucial for deciphering complex traits and diseases.
• Existing resources often lack integrative multi-omics data and fine-mapped regulatory variant information.

Purpose of the Study:

• To develop and present the Japan Omics Browser (JOB) for integrative analysis of human omics data.
• To provide visualization of per-variant regulatory effects at mRNA and protein levels.
• To offer regulatory effect prediction scores and validation data for genetic variants.

Main Methods:

• Statistical fine-mapping of expression quantitative loci (eQTL) and protein quantitative loci (pQTL) in a Japanese cohort (n=1,405).
• Integration of fine-mapping results for 94 complex traits from the UK Biobank.
• Multi-task learning to train per-tissue regulatory effect prediction scores (EMS).
• Inclusion of validation scores from Massively Parallel Reporter Assays (MPRA).

Main Results:

• JOB enables distinct visualization of mRNA and protein-level regulatory effects for variants in human blood.
• The browser incorporates fine-mapping results for numerous complex traits and provides EMS predictions.
• Over 10,000 variants are available with MPRA validation scores across two cell types.

Conclusions:

• JOB serves as a valuable resource for integrative analysis of human omics data.
• The platform facilitates the study of regulatory variants and their impact on complex traits.
• JOB enhances understanding of genotype-phenotype relationships through multi-omics integration and validation data.