ABSTRACT
This chapter demonstrates how to perform enrichment analyses of omic-wise association analysis. It focuses on over representation analysis approach which is commonly used in practice since it can be extended to any gene set as those defined, for instance, at Molecular Siganture Database. The chapter illustrates the practical issues of the approach on the transcriptomic study of Alzheimer’s disease. It outlines how to perform the type of analysis in the copy number settings where the outcome is a list of genomic ranges instead of genes. The aim of genome, transcriptome and epigenome-wide association studies is the identification of any variable, or groups of variables that is significantly associated with phenotypic differences among individuals. Enrichment analyses on association studies address the difficulties of interpretation and of statistical power. The chapter demonstrates how query annotation data from the human genome to retrieve the gene ontologies (GO) terms associated to a gene or the genes that belong to a given GO term.
