[BioC] Identifying Processes as Upregulated or Downregulated

[Joseph Shaw]

Hi all,

I am in the process of performing some ontological analysis with
GOstats. Given that GOstats doesn't require any information on
relative increases or decreases in expression for its hypergeometric
testing procedure, am I correct in assuming that it does not
differentiate between upregulated and downregulated genes?

If this is the case then providing a list of differentially expressed
genes (both upregulated and downregulated) to the testing procedure
will result in ontology results where upregulation and downregulation
may be confounded.
In other words, combining upregulated and downregulated genes and
comparing the resulting list to the gene universe will enable the
testing procedure to identify regulated ontological processes, but it
won't be able to identify whether the processes are upregulated or
downregulated. In fact, given that there is no distinction provided as
input, it may even be both.

To me, it seems that in order to prevent this from happening two
separate testing procedures should be performed: one comparing
upregulated genes to the gene universe and one comparing downregulated
genes to the gene universe. Is this approach advisable? Is there a
correct protocol which addresses the above issue?

Joseph