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Chunk #8 — Materials and Methods — Pathway Analysis — ALIGATOR [15]

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Pathway analysis of smoking quantity in multiple GWAS identifies cholinergic and sensory pathways.
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might tag a gene, each gene is counted only once. The statistical significance of the overrepresentation of each set of genes (category-specific p-value) is calculated by comparing the number of significant genes to the number of genes expected by chance. For this purpose, the algorithm generates 50,000 sets of genes, by randomly selecting SNPs until a list of n tagged genes is formed.