Need help with a chip-seq track in the UCSC browser

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Dhanasekaran, Mohan

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Jul 16, 2015, 12:11:24 PM7/16/15
to gen...@soe.ucsc.edu, Wang, George X.

Hello,

We are from the University of Michigan.  We were looking at the SYDH TFBS for NFKB transcription factor.  We were unable to select this dataset for any of the cell lines.  We tried selecting all TFs in this dataset, while other TF Chip-seq data displays, for some reason the NFKB track gets unselected.  Can you please help us?

 

 

http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=435314497_JZkIx92a0sXkcczGm4GjIZAjiBjA&c=chr1&g=wgEncodeSydhTfbs

 

Best

Mohan and George.

 

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Brian Lee

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Jul 16, 2015, 11:44:53 PM7/16/15
to Dhanasekaran, Mohan, gen...@soe.ucsc.edu, Wang, George X.
Dear Mohan and George,

Thank you for using the UCSC Genome Browser and your question about the SYDH TFBS track and selecting the NFKB experiments.

This very large matrix of experiments has an additional two levels of selection occurring at the bottom for treatment and control. All the NFKB experiments involve TNFa, and with default settings TNFa treatments are excluded and hence the NFKB experiments.

Here are some steps to take to select the NFKB experiments. First navigate to the track, http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeSydhTfbs , and click the "Reset to defaults" option. Next click the box for "[-] All" in the top corner of the matrix. Then scroll down and click the "NFKB [+]" box to select the row of NFKB experiments. Lastly, scroll to the bottom of the matrix and click into the "Treatment" box and select "All". Now the TNFa treatment experiments will be included, and the NFKB experiments will show up.

I want to also share that there is a "Track Search" feature, available under the main browser on the far left when looking at track data, that you can click. You can then perform advanced and simple searches. Advanced searches allow complicated selections on metadata about tracks. Here is a link where if you click search, it will perform a simple search on "NFKB" and find these tracks: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hgt_tSearch=1&tsCurTab=simpleTab&tsSimple=NFKB

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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Dhanasekaran, Mohan

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Jul 17, 2015, 12:31:01 PM7/17/15
to gen...@soe.ucsc.edu, Wang, George X.

Thank you Brian for the very helpful detailed email.  We are able to see the tracks now. I have two more questions

1.        Will the TCGA or other consortium datatracks from various cancer types be available to view in the UCSC browser? 

2.         I know you have UCSC tutorial videos, do you also give webminars to explain various features in the browser now (that keeps changing so rapidly!)  If yes I would like to set up a webminar with our group members.

Best

-Mohan

Matthew Speir

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Jul 17, 2015, 7:07:14 PM7/17/15
to Dhanasekaran, Mohan, gen...@soe.ucsc.edu, Wang, George X.
Hi Mohan,

For your first question, no, we do not have any plans to incorporate large amounts of TCGA data in the Genome Browser as native tracks. However, there is at least one public track hub that includes some data from TCGA and that is the "CPTAC Hub v1" available on the Hub connect page: http://genome.ucsc.edu/cgi-bin/hgHubConnect. This track hub provided by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) provides TCGA Mass Spec data from ovarian, colon and breast cancer samples. If you are interested in viewing cancer genomics data, I would recommend looking at the Cancer Genome Browser here at UCSC: https://genome-cancer.ucsc.edu/. Note that questions about the Cancer Genome Browser should be directed to them at https://genome-cancer.ucsc.edu/proj/site/contactUs.

For your second question, no, we currently do not host any "webinars", although we may sometime in the future. If you are interested, we do provide in-person workshops taught by one of our trainers. You can find more information on setting this up here: http://bit.ly/ucscTraining. Other than the short tutorial videos provided by the UCSC Genome Browser, http://genome.ucsc.edu/training/vids/index.html, you may be interested in the longer Open Helix tutorials: http://www.openhelix.com/ucsc. The tutorials provided Open Helix cover a range of topics from viewing your data in the Genome Browser to creating queries on the Table Browser.

I hope this is helpful. 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 Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group
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