[BioC] ChIPpeakAnno_2.8.0 assignCromosomeRegion

[Steve Lianoglou]

Hi

On Thu, Apr 25, 2013 at 6:27 AM, Zhu, Lihua (Julie)
<Julie.Zhu at umassmed.edu> wrote:
> Dear Mboyba,
>
> According to my understanding, intergenic regions consist of promoters,
> enhancers/silencers, noncoding RNAs and other unknown elements. Currently,
> any intergenic regions that are not promoter or immediate downstream are
> lumped into enhancer/silencer category. If you could help us define
> enhancers and other intergenic elements more accurately, then we can have a
> fine-grained partition of the intergenic region.

Although I am far from an expert in this domain, if I were a user of
this tool I'd probably expect peaks that land in non-genic,
non-promoter regions to be labeled as intergenic instead of
enhancer/silencer unless we have good evidence to suggest otherwise.

In my mind, calling something an ehancer or a silencer means something
very specific, where as labeling something as intergenic means that we
have no evidence to support it to be anything else.

Perhaps neither here nor there, perhaps GREAT might be of interest in
these scenarios (also never used it):

http://bejerano.stanford.edu/help/display/GREAT/Home
http://bejerano.stanford.edu/papers/GREAT.pdf

Also -- if we want to start really labeling things as
enhancer/silencer and have it mean something functional, perhaps an
annotation effort might be worthwhile where one would trawl several of
the recent papers coming out of John Stamatoyannopoulos' lab where
they leverage DNase-seq to find such regions (enhancers/silencers)
that are supported by differing degrees of experimental evidence.

HTH,
-steve

--
Steve Lianoglou
Computational Biologist
Department of Bioinformatics and Computational Biology
Genentech