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Demo run: GWAS SNP P value as demo input
The demo input is SNP P-value from the GWAS of HIV-1 host control [1] The P-value has been transformed to -log(P-value). With the default parameter of our i-GSEA4GWAS server [2], 5 pathways/gene sets namely "hsa04612 antigen processing and presentation", "inflampathway", "cskpathway", "hsa03010 ribisome", and "st myocyte ad pathway", were identified to be correlated to the trait of HIV-1 viral load set point with high confidence (FDR < 0.05).
[1] Fellay J, et al., A whole-genome association study of major determinants for host control of HIV-1. 2007, Science 317 (5840) 944-7. (Originally published in Science Express on 19 July 2007)
[2] The default parameters are: data type: SNP; SNPs->genes mapping rule: 500 kb upstream and downstream of gene; Gene set database: canonical pathways; keyword: Null; mask MHC/xMHC region: No; Number of genes in gene set: minimum 20, maximum 200.
Other sample input data:
1. Another example of SNP P-value data is from the GWAS of bipolar disorder (WTCCC, Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls Nature 2007). The P-value has been transformed to -log(P-value).
2. Gene association data (for HIV-1 host control and bipolar disorder)
The sample gene association data is derived from the mapping result of SNPs to genes by using the SNPs->genes mapping rule of ¡°500kb upstream and downstream of genes¡±. The association value of each gene is given by the maximum -log(P-value) of the SNPs mapped the gene.
3. Gene set sample data
The gene set sample data listing a few gene sets is to show an example of the format for users to prepare for their customized gene sets.
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