discusses approximate and exact tests for GO enrichment/depletion, the associated p-value computations, and Table 1 contains over 20 GO tools packages.
Bioinformatics 2007 23(4):401-407
http://bioinformatics.oxfordjournals.org/cgi/content/full/23/4/401
This paper’s been out for a while, not sure if we’ve seen it:
Polycomb group proteins are essential for early development in metazoans, but their contributions to human development are not well understood. We have mapped the Polycomb Repressive Complex 2 (PRC2) subunit SUZ12 across the entire nonrepeat portion of the genome in human embryonic stem (ES) cells. We found that SUZ12 is distributed across large portions of over two hundred genes encoding key developmental regulators. These genes are occupied by nucleosomes trimethylated at histone H3K27, are transcriptionally repressed, and contain some of the most highly conserved noncoding elements in the genome. We found that PRC2 target genes are preferentially activated during ES cell differentiation and that the ES cell regulators OCT4, SOX2, and NANOG cooccupy a significant subset of these genes. These results indicate that PRC2 occupies a special set of developmental genes in ES cells that must be repressed to maintain pluripotency and that are poised for activation during ES cell differentiation.
Cell. 2006 Apr 21;125(2):301-13.
