[BioC] ChIPpeakAnno_2.8.0 assignCromosomeRegion

[Umass]

Steve,

Great suggestions! Thanks for sharing!

Best regards,

Julie

On Apr 25, 2013, at 2:18 PM, Steve Lianoglou <mailinglist.honeypot at gmail.com> wrote:

> 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