Features

Load GWAS data in various formats (.tab, .ped, .syn).

Use Gene Ontology to select subset of SNPs to analyze.

Search for most informative single SNPs.

Search for synergistically interacting pairs of SNPs.

Draw synergy (interaction gain) and information gain distributions.

Estimate significance by performing random permutation analysis.

Explore annotation of most informative single SNPs and pairs of SNPs.

Perform Gene Ontology term enrichment analysis on genes associated with selected SNPs.

Build and explore SNP interaction networks.

What is SNPsyn?

SNPsyn is an exploratory gene interaction analytics application. It helps you discover and quantify the synergy of SNP-SNP interactions in case-control Genome-Wide Association Studies (GWAS) data.

Click here to quickly start playing with SNPsyn.

You may view some other prepared examples before submitting your own data.

How to cite?

If you use SNPsyn in your research, please cite:
T. Curk, G. Rot, and B. Zupan (2011). SNPsyn: detection and exploration of SNP–SNP interactions. Nucl. Acids Res. 39(suppl 2): W444-W449, doi:10.1093/nar/gkr321.

Screenshots


Prepare and load data.
Select SNPs for analysis.

Select interacting SNPs.
List synergistic SNP-SNP interactions.

Gene Ontology enrichment analysis.
Explore the gene interaction network.
© 2011 Bioinformatics Laboratory
University of Ljubljana, Faculty of Computer and Information Science