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snpXplorer: a web application to explore human SNP-associations and annotate SNP-sets
Niccolo Tesi1,2,3, Sven van der Lee1,2, Marc Hulsman1,2,3
1Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands.
snpXplorer simplifies the analysis of genetic association studies by integrating multiple data sources for Single Nucleotide Polymorphisms (SNPs). This web tool aids researchers in interpreting complex genetic data across various human phenotypes.
Area of Science:
- Genomics
- Bioinformatics
- Human Genetics
Background:
- Genetic association studies are crucial for understanding the genetic basis of human phenotypes.
- Interpreting genetic associations and assessing genomic regions across traits is complex, requiring advanced bioinformatics skills and data integration.
Purpose of the Study:
- To develop an accessible web-server application, snpXplorer, for exploring Single Nucleotide Polymorphism (SNP) association statistics and functional annotation.
- To facilitate the interpretation of genetic associations by integrating diverse genomic data and enabling cross-trait comparisons.
Main Methods:
- Developed snpXplorer, a user-friendly web server for SNP analysis.
- Integrated multiple association statistics, regional information (structural variations, recombination rates, eQTL, LD), genes, and gene expression data.
- Implemented variant-to-gene mapping and gene-set enrichment analysis for functional interpretation.
Main Results:
- snpXplorer allows superposition of association statistics from multiple studies, enabling comparison across traits.
- The tool displays comprehensive regional genomic information alongside SNP associations.
- Enables identification of overrepresented molecular pathways through gene-set enrichment analysis.
Conclusions:
- snpXplorer provides an easy-to-use platform for researchers to explore and interpret complex genetic association data.
- Facilitates functional annotation of SNPs and pathway analysis, advancing the understanding of genetic influences on human phenotypes.
- The freely available tool and its resources aim to lower the barrier for advanced genetic data interpretation.
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