Gene Enrichment Programs
BABELOMICS v3.0
http://babelomics.bioinfo.cipf.es/
GAA
http://gaa.mpi-bn.mpg.de/
Gene Set Analysis
http://www-stat.stanford.edu/~tibs/GSA/
GeneTrail
http://genetrail.bioinf.uni-sb.de/
GSEA
http://www.broad.mit.edu/gsea/
GSEA MSigDB
http://www.broad.mit.edu/gsea/msigdb/index.jsp
GSEA MSigDB Browse Gene Sets
http://www.broad.mit.edu/gsea/msigdb/genesets.jsp?letter=A
H-InvDB Enrichment Analysis Tool
http://hinv.jp/HEAT/search.php?lang=en
limma
http://www.bioconductor.org/packages/1.9/bioc/html/limma.html
PGE
http://homes.esat.kuleuven.be/~bioiuser/pge/
SAM-GS
http://www.ualberta.ca/~yyasui/homepage.html
T-Profiler @ Bussemaker Lab
http://www.t-profiler.org/
webgestalt Web-based Gene Set Analysis Toolkit
http://bioinfo.vanderbilt.edu/webgestalt/