# GeneSetPheno: a web application for the integration, summary, and visualization of gene and variant–phenotype associations across gene sets

## TL;DR

GeneSetPheno is a web tool that helps researchers explore and visualize how genes and genetic variants are linked to different traits or diseases.

## Contribution

It introduces a user-friendly interface for integrating and comparing gene-phenotype associations across multiple genomic resources.

## Key findings

- GeneSetPheno enables the exploration of genetic variant-phenotype relationships within user-defined gene sets.
- The tool supports comparisons across gene sets to identify shared or unique associations and biological pathways.
- It provides a free and configurable platform for molecular biologists and clinicians to analyze complex genetic data.

## Abstract

The comprehensive study of genotype-phenotype relationships requires the integration of multiple data types to “triangulate” signals and derive meaningful biological conclusions. Large-scale biobanks and public resources generate a wealth of comprehensive results, facilitating the discovery of associations between genes or genetic variants and multiple phenotypes. However, analyzing these data across resources presents several challenges, including limited flexibility in gene set analysis, the integration of multipe databases, and the need for effective data visualization to aid interpretation.

GeneSetPheno is a user-friendly graphical interface that integrates, summarizes, and visualizes gene and variant-phenotype associations across genomic resources. It allows users to explore interrelationships between genetic variants and phenotypes, offering insights into the genetic factors driving phenotypic variation within user-defined gene sets. GeneSetPheno also supports comparisons across gene sets to identify shared or unique genetic variants, phenotypic associations, biological pathways, and potential gene-gene interactions. GeneSetPheno is a free and highly configurable tool for exploring the complex relationships between gene sets, genetic variants, and phenotypes. Target users include molecular biologists and clinicians who wish to explore a gene or gene set of particular interest.

GeneSetPheno is freely accessible at: https://shiny.wehi.edu.au/han.ji/GeneSetPheno/. The source code is available on GitHub at: https://github.com/bahlolab/GeneSetPheno.