Gene set analysis methods: a systematic comparison.

ABSTRACT:

Background

Gene set analysis is a valuable tool to summarize high-dimensional gene expression data in terms of biologically relevant sets. This is an active area of research and numerous gene set analysis methods have been developed. Despite this popularity, systematic comparative studies have been limited in scope.

Methods

In this study we present a semi-synthetic simulation study using real datasets in order to test and compare commonly used methods.

Results

A software pipeline, Flexible Algorithm for Novel Gene set Simulation (FANGS) develops simulated data based on a prostate cancer dataset where the KRAS and TGF-β pathways were differentially expressed. The FANGS software is compatible with other datasets and pathways. Comparisons of gene set analysis methods are

SUBMITTER: Mathur R 

PROVIDER: S-EPMC5984476 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature