layered H3K27Me3 data

[Alice Uwineza]

Dear Sir/ Madam,

I have been working with the layered H3K27Ac and H3K4Me1 UCSC data to verfiy where these protein bind on the genes (e.g. http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr6%3A36644237-36655116&hgsid=415450677_IkCj2G1V7NaYKbxTMSHbjGemPgNw ). Now I would like to add a layered H3K27Me3 data, so that when I type in a specific gene I can verify where it is generally trimethylated. I got as far as finding all the available H3K27Me3 data: http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=415450677_IkCj2G1V7NaYKbxTMSHbjGemPgNw&hgt_=1425491354&db=hg19&tsCurTab=simpleTab&hgt_tsDelRow=&hgt_tsAddRow=&hgt_tsPage=&tsSimple=H3K27me3&hgt_tSearch=search&tsName=&tsDescr=&tsGroup=Any&tsType=Any&hgt_mdbVar1=cell&hgt_mdbVal1=Any&hgt_mdbVar2=antibody&hgt_mdbVal2=Any but I don't know how to create a layered version of this data. Could you please help me out?

I will be grateful for any help you can provide

Alice

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Alice Uwineza, MSc
PhD Student,
O'Sullivan Research Group

The National Children's Research Centre
Our Lady's Children's Hospital, Crumlin, Gate 5
Dublin 12
IRELAND

Email: uwin...@tcd.ie

Phone: 00353 (01) 409 6421

[Brian Lee]

Dear Alice,

Thank you for using the UCSC Genome Browser and your question about layered H3K27Me3 data.

The Layered H3K27Ac track you are displaying, http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegMarkH3k27ac, is one of many Integrated Regulation Tracks from ENCODE in the browser, that is grouped in a larger "super-track". On the Track Description page for the "Layered H3K27Ac" page, you can find a "(ENCODE Regulation)" link, that will take you to this top super-track.

Or you can click this link, http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeReg, to arrive at the top "ENCODE Regulation Super-track Settings" page. Note the Integrated Super-track also has a clustered Txn Fact ChIP and Transcription RNA-seq track, and a "Layered H3K4Me3" track, http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegMarkH3k4me3, which I believe is not quite the track you desire.

While a layered integrated H3K4Me3 track exists, one doesn't exist for H3K27Me3, explaining why it did not come up in your track search.

But you can create one by putting the bigDataUrls to the desired underlying bigWigs (which would should be uniformly processed) into a track hub and using the multiwig feature:http://genome.ucsc.edu/goldenPath/help/hubQuickStartGroups.html Because you should use uniformly processed data, you should likely use the externally provided ENCODE Analysis Working Group Uniform Histone Hub files:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&hubUrl=http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt&g=hub_4607_uniformHistone

In essence your Track Hub trackDb.txt would look like this example multiwig at the top of this trackDb.txt:
http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubGroupings/hg19/trackDb.txt

But where the bigDataUrls in each point to the AWG Hub Files located in their trackDb.txt:http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hg19/trackDb.txt

Here is a starter Multi Wig Hub, where those steps have been taken for three files:
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://hgwdev.cse.ucsc.edu/~brianlee/tempDelete4/hubExamples/hubGroupings/hub.txt

For example, if you look at this starter trackDb.txt, it only has three AWG bigWigs just for K562 H3K27me3, data in the "bigDataUrl" lines:
http://hgwdev.cse.ucsc.edu/~brianlee/tempDelete4/hubExamples/hubGroupings/hg19/trackDb.txt

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genome Bioinformatics Group

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