Estimation of Gene Induction Enables a Relevance-Based Ranking of Gene Sets

In order to handle and interpret the vast amounts of data produced by microarray experiments, the analysis of sets of genes with a common biological functionality has been shown to be advantageous compared to single gene analyses. Some statistical methods have been proposed to analyse the differential gene expression of gene sets in microarray experiments. However, most of these methods either require threshold values to be chosen for the analysis, or they need some reference set for the determination of significance. We present a method that estimates the number of differentially expressed genes in a gene set without requiring a threshold value for significance of genes. The method is self-contained (i.e., it does not require a reference set for comparison). In contrast to other methods which are focused on significance, our approach emphasizes the relevance of the regulation of gene sets. The presented method measures the degree of regulation of a gene set and is a useful tool to compare the induction of different gene sets and place the results of microarray experiments into the biological context. An R-package is available.