Transcription factors data

[Andrea Clocchiatti]

Dear Encode consortium,
I'm Andrea Clocchiatti a postdoc interested in your great data set.
I'd like to know if theme is a tool to see all the bindings of a transcription factor (in this case Mef2A), and their corresponding genes.
If you were so kind to indicate how to identify the mef2 regulated genes in your datasets it would be very useful.
Thanking you in advance of the time dedicated and your helpfulness,
Best regards
a

[Brian Lee]

Dear Andrea,

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

Please know the website for up-to-date information about the ENCODE project is no longer hosted at www.genome.ucsc.edu/ENCODE, rather the current ENCODE Consortium portal is located at https://www.encodeproject.org/ with a mailing list address of encod...@lists.stanford.edu. There are many resources on the consortium portal page including information about software tools for applying and analyzing ENCODE data: https://www.encodeproject.org/software

However, on the UCSC Genome Browser you can still access ENCODE data from the period of 2003 - 2012, and our ChIP-seq matrix helps to identify what factors are available, and the summary page allows you to click to all related results:

http://genome.ucsc.edu/ENCODE/dataMatrix/encodeChipMatrixHuman.html

http://genome.ucsc.edu/ENCODE/dataMatrix/encodeDataSummaryHuman.html

Looking at the summary page you will see there are 3 experiments involving MEF2A.  By clicking through on the MEF2A link you can see there are 14 data tracks available (by selecting the radio button for files on that  page, you can rather display all the files for immediate download). While these are the raw data tracks of MEF2A data, if you are looking for a more summarized display you can go to the uniform TFBS track that processed all underlying files through a computational pipeline.  You can read more (and select only MEF2A from the "Filter by factor" option) on this page: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV3

Here is a session with the MEF2A uniform peaks displayed under the UCSC Genes Track and the underlying raw data also displayed: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=MEF2A.Display

You can use our Table Browser, http://genome.ucsc.edu/cgi-bin/hgTables,  to do an intersection on this displayed data. It involves several steps.  First you would create a custom track of the MEF2A regions and then intersect that custom track with the Gene Prediction track of interest.

1. Go to the Table Browser and select hg19, group: Regulation, track: Txn Factor ChIP, with region: genome selected

2. Click the filter: create button, and in "name does match" put the following: MEF2A

3. Click the submit button and then change output format to custom track and get output, and then click "get custom track in table browser"

You now have a custom track of all the MEF2A locations across the hg19 assembly.  You can now do an intersection with a gene track.

1. Select group: Genes and Gene Predictions, track: UCSC Genes (or other gene track)

2. Click the intersection: create button

3. Change the group on the intersection page to Custom Tracks and use the track name just created in the last step, click submit

4. Change output to custom track and "get custom track in genome browser" and you will now just have the UCSC genes that have MEF2A intersections with their coding regions (it will exclude intersection with introns).

You can watch a tutorial about the Table Browser here to learn more about creating custom tracks and doing further intersections: http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28

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

--