Onto-Tools is a freely available web-accessible software suite, composed of an annotation database and nine complementary data-mining tools. This article describes a new tool, Onto-Express-to-go (OE2GO), as well as some new features implemented in Pathway-Express and Onto-Miner over the past year. Pathway-Express (PE) has been enhanced to identify significantly perturbed pathways in a given condition using the differentially expressed genes in the input. OE2GO is a tool for functional profiling using custom annotations. The development of this tool was aimed at the researchers working with organisms for which annotations are not yet available in the public domain. OE2GO allows researchers to use either annotation data from the Onto-Tools database, or their own custom annotations. By removing the necessity to use any specific database, OE2GO makes the functional profiling available for all organisms, with annotations using any ontology. The Onto-Tools are freely available at http://vortex.cs.wayne.edu/projects.htm.