7 Gene Set Enrichment Analysis in Genomics

7.1 Overview

Given a list of genomic regions, what are the biological functions they relate. A nature solution is to first annotate genomic regions to the nearest TSS, then only use genes with a certain distance for ORA analysis. In this chapter, we will discuss the problems of directly apply ORA on genomic data and the solutions.

7.2 The GREAT method

7.3 The rGREAT package

7.4 The Lola package

7.5 RNASeq and methylation-adjusted ORA

7.6 SNP-based GSEA

7.7 general comments

E.g. large sample size

compare between different sets of genomic regions