SNP-based Pathway Enrichment Analysis for Genome-wide Association Study

"SNP-based Pathway Enrichment Analysis for Genome-wide Association Study"; Lingjie Weng, Fabio Macciardi, Aravind Subramanian, Guia Guffanti, Steven G. Potkin, Zhaoxia Yu, Xiaohui Xie

Copyright (C) 2010 Lingjie Weng

The code is implemented with Java. The demonstration code can be found here: download SSEA.

Instruction of use

Input files: ( Example input files can be found here: example files.

1) SNP genotype file

The first line contains the SNP ID and a list of phenotype of the subjects,Ca if the subject belongs to case(disease) group, Co if the subject belongs to control group.

Line format: SNP_ID(tab)(subject 1 phenotype)(tab)(subject 2 phenotype)(tab) ... (subject N phenotype)

Example：SNPID Ca_1 Co_1 Co_2 Co_3 Ca_2 ...

The remainder of the data file contains data for all SNPs. Rows corresponds to SNPs, columns corresponds to genotype(use 1,2,3 to represent 3 different genotypes AA, AB,BB; use 0 to represent the missing genotype data).

Example: rs12082473 1 0 1 1 3 ...

2) SNP to Gene Mapping file (annotation file)

Example: SNPId Gene_Name

3) Pathway file(the gene sets used for testing were downloaded together with the original GSEA software from KEGG)

Example: Pathway_Name annotation Gene_Name1 Gene_Name2 Gene_Name3 ... 3) Phenotype file(this can be obtain from the first line of SNP genotype file, look for example file for detail)

This package has two steps: it first use SNP genotype file and annotation file to generate Significant SNP files; together with pathway(SNPset) file would be used as an input for the second step. The final output file include the pathway name, pathway size, enrichment score and nominal p-value.