Gene Ontology analysis is not without its own pitfalls. Besides the obvious effects of overlapping annotations for the majority of genes and annotation bias, the categories themselves often do not describe real biological phenomena. Given that transcription factors are very cell-type specific, a category that includes all of them is not particularly useful. In light of this, the q-values for transcription factor-related categories are likely to be overly conservative, and would probably be smaller if those TFs not expressed in this tissue were excluded. Future studies could address this problem using array and wet lab expression data.
