Table 1.

Summary of g:Profiler features in 2007 and novel additions in 2011

Feature	g:Profiler 2007	Added in g:Profiler 2011
Supported species	31 species Ensembl	85 species Ensembl and Ensembl genomes, mammals, fungi, insects, plants, etc.
Biological evidence considered	Gene ontology Pathways databases (KEGG, Reactome) Transcription factor motifs (Transfac) Gene expression similarity search (GEO)	microRNA target sites (MicroCosm) Disease genes (HPO) Protein–protein interactions (BioGrid) Gene expression similarity search (ArrayExpress)
Input for enrichment analysis	Gene sets Ordered gene lists Functional groups	Chromosomal regions Multiple gene lists or regions
Methods	Hypergeometric test Multiple testing (g:SCS, FDR, Bonferroni)	Customized background set Enrichment of interaction network modules
Tools	g:GOSt—gene group functional profiling g:Convert—gene ID converter g:Sorter—expression similarity search g:Orth—orthology search	g:Cocoa—compact comparison of gene annotations