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annotating to pseudogenes

Fiona McCarthy fmccarthy at cvm.msstate.edu
Tue Mar 14 08:35:25 PST 2006


Hi All,

I recent found a microarray tiling paper (PMID: 15876366) where the
authors estimated that one fifth of human pseudogenes on chr22 are
potentially transcribed. It seems to me that there must be a reason for
this level of transcription, even if we don't know what it is.

I think it would be reasonable to annotate pseudogenes to GO, even if we
have to use function unknown in most cases. Otherwise, we would be
implying that *all* pseudogenes have no function, and this may not be the
case.

As for the SO definition of a pseudogene, I am not sure that I would say
that all pseudogenes are non-functional.

Fiona


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