Data Access

VarXOmics is a versitile web server for genomic data querying and variants analysis and priortisation. The data sources are integrated from diverse open-source databases, including multi-omics informations (eQTL, pQTL, GWAS, Traits), pharmacogenomics infomration, protein-protein interactions, gene-drug interactions. The detailed data could be accessed as described followed:

Multi-Omics insights

1) eQTL

GTEx eQTL: GTEx v10-eQTL.

eQTL Catalog: eQTL/sumstats.

Pre-calculated scores: Data Access/pre-calculated eQTL scores.txt Scores are calculated only with significant eQTL results.

2) pQTL and MR

EpiGraphDB Data are retrieved by epigraphdb-r.

Pre-calculated scores: Data Access/pre-calculated pQTL scores.txt Scores are calculated by considering significant pQTL results and high-confidence protein-protein coexpression interactions.

3) GWAS

GWAS Catalog: GWAS Catalog (Version: 1.0-associations_e113_r2025-04-28).

4) Tratis

Curated trait list: Data Access/Trait lists.txt The list contains summary statistic for Athleticism, Behavior, Cardiovascular, Hormones, Immune System, Longevity, Metabolism, Nutrition and Diet, Physical Appearance, Sensory Perception, Wellness, Neurogenic and Cognitive functions, and Personality traits.

Pharmacogenomics

PharmGKB: PharmGKB (Version: 2025-May-05).

PharmGKB-pediatric drug information: PharmGKB (Version: 2024-May-15).

PharmVar: PharmVar (Version: 6.1.2).

Gene-Drug Interactions

Gene-Drug interaction database: DGIdb (Version: 2025-May).

Protein-Protein Interactions

STRING database: STRING-homo spaiens (Version: 12.0).

Gene expression levels in different tissues

Human Protein Atlas: HPA, which includes RNA expression (consensus) (50 tissues) and RNA expression (HPA) (40 tissues).

GTEx v10: GTEx v10-RNA bulk_tissue_expressionl.

Gene-Disease list

Curated gene-disease list: Data Access/Gene-Disease panel.xlsx It consists of lists from ACMG secondary findings v3.2, lists for carrier screening and newborn screening.

Software requirements:

Small varinat querying and analysis is conducted using Ensembl Variant Effect Predictor (VEP) (e114), while structural variants are analysed by AnnotSV (v3.4). The pipeline for data management and scoring sytem is built on R(v4.3.3) and and python (v3.12).