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/16aff253720865d2384b56b61a3f1816with >> 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 >> >> >> _______________________________________________ >> Users mailing list >> [email protected] >> https://lists.biomart.org/mailman/listinfo/users >> >> > > > -- > > 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. > >
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