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geneXplore: An Interactive Browser for X Chromosome-Wide Association Study Results
Medrxiv : the Preprint Server for Health Sciences
|July 30, 2026
Summary
We developed geneXplore, a novel web browser for X chromosome-wide association study (XWAS) summary statistics. This tool facilitates the investigation of X-linked genetic contributions to human traits, accounting for XCI escape and sex differences.
Area of Science:
- Genetics
- Genomics
- Human Biology
Background:
- The X chromosome contains over 800 genes, many with sex-differentiated expression due to X chromosome inactivation (XCI).
- X chromosome is often excluded from genome-wide association studies (GWAS) due to analytical complexities.
- Limited exploration of XCI escape and sex effects in GWAS hinders understanding of sex differences in complex traits.
Purpose of the Study:
- To introduce geneXplore, a dedicated web browser for X chromosome-wide association study (XWAS) summary statistics.
- To provide a platform for systematic investigation of X-linked genetic contributions to human traits.
- To enable analysis distinguishing random XCI (rXCI), escape from XCI (eXCI), and sex-stratified results.
Main Methods:
- Developed geneXplore using the PheWeb2 implementation.
- Integrated XWAS summary statistics for 1,944 phenotypes.
- Incorporated interactive visualization tools (Manhattan, Miami, PheWAS, LocusZoom) and searchable tables.
Main Results:
- geneXplore offers comprehensive exploration of XWAS data.
- The browser distinguishes results based on rXCI, eXCI, and sex stratification.
- Users can download full summary statistics and perform cross-database lookups.
Conclusions:
- geneXplore addresses the lack of a dedicated XWAS browser.
- Facilitates deeper understanding of X-linked genetic influences on human traits.
- Promotes systematic research into sex differences in complex diseases.
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