Before revision:  We propose PNEA, an alternative test based on the hypergeometric distribution . PNEA can be applied also to directed and mixed networks , and our simulations show that it is faster and more powerful than existing NEA tests.
After revision:  We propose PNEA, an alternative test based on the hypergeometric distribution . PNEA can be applied not only to undirected, but to directed and partially directed networks as well. Our simulations indicate that NEAT is considerably faster than alternative resampling-based methods, and that its capacity to detect enrichments is at least as good as the one of alternative tests. We discuss applications of NEAT to network analyses in yeast by testing for enrichment of the Environmental Stress Response target gene set with GO Slim and KEGG functional gene sets, and also by testing for associations between GO Slim categories themselves. NEAT is a flexible and efficient test for network enrichment analysis that aims to overcome some limitations of existing resampling-based tests.