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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...

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Related Experiment Video

Updated: May 23, 2026

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

SNPpath: characterizing cattle SNPs by enriched pathway terms.

Qishan Wang¹, Minghui Wang, Yumei Yang

¹School of Agriculture and Biology, Shanghai Jiao Tong University, China.

Animal Science Journal = Nihon Chikusan Gakkaiho

|April 21, 2012

Summary

This summary is machine-generated.

SNPpath is a new web server that annotates cattle single nucleotide polymorphisms (SNPs) with KEGG pathway terms. This tool aids in analyzing complex genetic traits by integrating SNP data with pathway analysis for genomic selection.

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Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

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Area of Science:

Genomics
Bioinformatics
Animal Genetics

Background:

High-density SNP microarrays enable large-scale Genome-Wide Association Studies (GWAS) and Genomic Selection (GS).
Understanding complex polygenic traits requires simultaneous analysis of functionally related gene sets.
Current tools lack comprehensive pathway annotations for cattle SNPs across major databases.

Purpose of the Study:

To develop and describe SNPpath, a web server for automatic annotation and characterization of cattle SNPs.
To provide pathway annotations using KEGG (Kyoto Encyclopedia of Genes and Genomes) terms.
To facilitate the analysis of large SNP sets and integration with pathway-driven gene set enrichment analysis.

Main Methods:

Development of a web server suite (SNPpath) for SNP annotation.
Enrichment of cattle SNPs with KEGG pathway terms.
Integration with NCBI's dbSNP database and three commercial SNP platforms.

Main Results:

SNPpath successfully annotates and characterizes cattle SNPs with enriched KEGG pathway terms.
The web server allows users to navigate and analyze large SNP sets efficiently.
SNPpath is the only current web server offering pathway annotations for cattle SNPs across specified databases.

Conclusions:

SNPpath provides a valuable resource for cattle genetic research by linking SNPs to biological pathways.
The tool is beneficial for combining SNP association analysis with pathway-driven gene set enrichment analysis.
SNPpath is freely available, promoting broader use in genomic selection and genetic studies.