Hi Tomithy
Yes that is correct.
Cheers
Rhoda
On 28 Mar 2012, at 23:04, Tomithy Too wrote:
Hi Rhoda,
Thanks for your reply and the help from ensembl's regulation team.
I would just like to restate a point to confirm it:
In the Regulatory evidence query: Can i expect to get Raw
experimental annotation of DNA interaction region with different
CellTypes and Assays. Eg. ENCODE data. This information would be
cleaned up experimentally, eg removing noise, but not filtered by
the process of building regulatory features.
Cheers
Tomithy
On Wed, Mar 28, 2012 at 11:16 PM, Rhoda Kinsella <[email protected]>
wrote:
Hi Tomithy
I have contacted a member our Regulation team and he says:
This is essentially correct. Almost all of the TFs present in the
evidence will have been used to build the regulatory features (some
may have been omited as we have some filters based on peak length).
The situation is slightly different for the histone evidence, there
will be a higher proportion not represented by a regulatory feature,
as they are only incorporated when they overlap a TF or site of open
chromatin (DNase1/FAIRE).
I hope that helps, but if you have further questions please don't
hesitate to ask
Regards
Rhoda
On 27 Mar 2012, at 16:07, Arek Kasprzyk wrote:
Hi Tomithy,
i cc'ing Ensembl experts to help you with your question
a
On Tue, Mar 27, 2012 at 1:47 AM, Tomithy Too
<[email protected]> wrote:
Hi Biomart Admin,
I am currently using the biomart services to obtain transcription
factor information for my project. I would like to know the
difference between the information that I obtain were I to fillup
the regulatory features vs regulatory evidence portion of the query
form (http://www.ensembl.org/biomart/martview/16aff253720865d2384b56b61a3f1816
with db=Ensembl Regulation 66 for Homo sapiens). This is what I
have gathered thus far:
Regulatory features: A set of consolidated and computed regulatory
regions supported by different raw experimental data. It's
available for each different cell line.
Regulatory evidence: Raw experimental annotation of DNA interaction
region with different CellTypes and Assays. Eg. ENCODE data.
I have read through the documentation at the following url but
would like to confirm this.
http://www.ensembl.org/info/docs/funcgen/index.html
http://www.ensembl.org/info/docs/funcgen/regulatory_build.html
Many thanks
Tomithy
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--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.
Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.
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