[BioC] Identifying Processes as Upregulated or Downregulated

[Joseph Shaw]

Hi Jim,

Thanks for your reply.

My worry, originally, was that that failure to differentiate between
upregulated and downregulated processes would lead to spurious
results.

Let's create another scenario. Assume we have a group of genes
identified as upregulated and another group of genes identified as
downregulated. Furthermore, assume two subsets: one belonging to the
upregulated group and one belonging to the downregulated group. Each
subset is associated with several GO terms including one GO term which
is common to both subsets - let's call this common term GO_A.
Now, it may be the case that, individually, when tested against a
defined gene universe, neither subset yields statistically significant
results for GO_A, but combining the aforementioned subsets and testing
against a gene universe does, in fact, yield a statistically
significant result for GO_1.
Let's assume that the process represented by GO_A is such that it
cannot be simultaneously upregulated and downregulated; if this is the
case, wouldn't it be incorrect to combine the upregulated and
downregulated gene lists?

Let's return to the example provided in your previous mail.
My understanding of the GO DAG is far from exhaustive, so it's very
possible that I'm wrong, but, given that the GO terms become more
specific as we move towards leaf nodes, would we eventually arrive at
a terms representative of negative regulation of programmed cell death
and positive regulation of programmed cell death?
If this is the case, assuming there was a sufficient amount of genes
identified as differentially expressed for both enhancer (identified
as upregulated in our experiment) and preventer (identified as
downregulated in our experiment) genes so as to yield statistically
significant results for separate tests. Would it be incorrect to
conclude that negative regulation of preventers of programmed cell
death and positive regulation of enhancers of programmed cell death
have both been shown to be statistically significant significant? It
seems to me that both these results are compatible.

Joseph

On Tue, Feb 11, 2014 at 2:00 PM, James W. MacDonald <jmacdon at uw.edu> wrote:
> Hi Joseph,
>
> I think you are making a simplifying assumption that isn't helpful. In other
> words, you are assuming that up-regulation of a set of genes means something
> different than down-regulation, or a mixture thereof. But this flies in the
> face of much that we know about biological processes.
>
> As an example, say we have a set of genes with 'programmed cell death' as
> their GO term. And further assume that some of these genes enhance this
> process, and some prevent the process. Now if most of the enhancers are
> up-regulated, and most of the 'preventers' are down-regulated, are you
> prepared to say these genes should be tested separately because the
> up-regulated genes are involved with a different process than the
> down-regulated genes?
>
> Best,
>
> Jim
>
>
>
>
> On Monday, February 10, 2014 6:43:52 PM, Joseph Shaw wrote:
>>
>> 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
>>
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099