Gene Set Enrichment and Pathway Analysis

DAVID has been a go-to for gene set analysis since 2009. It retrieves enrichment results for an uploaded list of genes in dozens of different databases: Gene Ontology, protein interactions, disease annotations, pathways, and much more. It also has a useful gene ID conversion tool. It does not accept upload of experimental data with expression values. DAVID is web-based, though the knowledgebase is available to download.

Reactome's web interface accepts both gene lists and experimental data uploads, and performs enrichment analyses of your uploaded objects, outputting a list and visual representation of canonical pathways represented in your list. It also has a desktop application for integration with Cytoscape, so you can create networks based on your interaction analyses.

From UCSD and the Broad Institute, GSEA is a downloadable software platform for enrichment analysis on a set of genes. GSEA integrates the Molecular Signatures Database (MSigDB) to select the background list of genes to use for your analysis. You can input a list of genes, or upload your experimental data. Results can be exported and used in a network visualization package such as Cytoscape.

For those who don't want to install software for GSEA on their computers, the makers of GSEA also offer GenePattern, which is a web-based GSEA platform on an Amazon cloud instance that allows much of the same analyses as GSEA, plus many other types of analyses (SNP, RNA-Seq, clustering, etc). It also helps you build a pipeline that can be saved and shared for reproducible research results. You must register a username and password for use of GenePattern.