Showing posts from May, 2020

Mitch: An R package for Multi-Contrast Gene Set Enrichment Analysis

Gene set enrichment is one of the key methods in the understanding of gene expression patterns. As omics are becoming more widely used, large experiments are common and include not just one contrast (control vs case), but perhaps many contrasts (eg: healthy, disease, treatment 1, treatment 2, etc). Previously, as part of an epigenetics/epigenomics lab we were looking at ways to integrate different types of omics profiling such as RNA expression, histone acetylation and DNA methylation. We stumbled across a paper that proposed the use of multivariate ANOVA on ranks ( Cox & Mann 2012 ) to identify gene sets that exhibited enrichment in one or more contrasts. We thought this could be a simple way to identify gene set enrichments when looking at multiple contrasts without the need to run GSEA multiple times and summarise the results. The tool described in Cox & Mann (2012) is written for the Perseus suite which works for Windows. We saw there was no similar implementation in R so