mouse data

[Ahmed Arslan]

Hi,

I need to retrieve genomic locations of TF binding sites, promoters, enhancers, silencers, can you please guide me how I can download these data? Thanks.

best,

Ahmed Arslan, MS. Ph.D.

Postdoctoral Scholar 

300 Pasteur Drive, Grant Building,
Stanford, CA 94305

Twitter: https://twitter.com/AhmedArslan

Github: https://github.com/AhmedArslan

[Jairo Navarro Gonzalez]

Hello Ahmed,

Thank you for using the UCSC Genome Browser and your inquiry.

You may find the Track Search tool useful to find native tracks with these elements.
You can read how to use the tool from the following help page:

http://genome.ucsc.edu/goldenPath/help/trackSearch.html

There are also track hubs available that have these annotations for mm10, such as the
Ensembl Regulatory Build hub. For example, searching for TFBS on the Track Hubs page,
you can find hubs that contain relevant tracks for mouse.

For the mm10 assembly, you may find the NCBI Functional Elements track useful:

Elements in scope include experimentally-verified gene regulatory regions
(e.g., enhancers, silencers, locus control regions), known structural elements
(e.g., insulators, DNase I hypersensitive sites, matrix/scaffold-associated regions),
well-characterized DNA replication origins, and clinically-significant sites of DNA
recombination and genomic instability.

Since the RefSeq Functional Elements track contains many different types of annotations,
you will want to use the Table Browser to filter the track down to only your elements of interest.

i.e., soTerm does match enhancer.

We also have downloadable ENCODE data available for mm9:

https://genome.ucsc.edu/encode/downloadsMouse.html

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.

Jairo Navarro 
UCSC Genomics Institute

Want to share the Browser with colleagues?

Host a workshop: http://bit.ly/ucscTraining

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[Ahmed Arslan]

Thank you very much, Jairo for the information. However, I need to download these functional data (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm10&g=refSeqFuncElems)  in a tab-separated or any text format for my analysis. Can you please help me with it?

Thanks

best,

Ahmed Arslan, MS. Ph.D.

Postdoctoral Scholar 

300 Pasteur Drive, Grant Building,
Stanford, CA 94305

Twitter: https://twitter.com/AhmedArslan

Github: https://github.com/AhmedArslan

---

From: Jairo Navarro Gonzalez <jnav...@ucsc.edu>
Sent: Tuesday, March 6, 2018 7:27:01 AM
To: Ahmed Arslan
Cc: gen...@soe.ucsc.edu
Subject: Re: [genome] mouse data

 

[Brian Lee]

Dear Ahmed,

Thank you for using the UCSC Genome Browser and your question about extracting data for the refSeqFuncElems track.

The easiest way to extract this data is to use the Table Browser as Jairo shared in the previous message. If you go to the top blue bar, under Tools you will find a link to the "Table Browser." The best way to access the Table Browser is when you have already navigated to the Track Description page, such as the link you previously shared, then the Browser knows to intelligently fill out all the appropriate fields so you can access the correct Table for that data.

For example, if you went to the Table Browser, you could set the 
"group:" to "Expression and Regulation" and then the "track:" to "RefSeq Func Elems" and then the table would select refSeqFuncElems. Then you could click the "get output" link or make choices on how the output format should look (such as only selected desired fields) and you could put a name in the "output file:" section such as done in this example: http://genome.ucsc.edu/cgi-bin/hgTables?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=mm10_regulatory_build

By clicking the "get output" on that session link, you will download a file that has the name "fileNameForRefSeqFuncElems" inputted into the "output file" section.

This example session shared also has an external hub connected, the "Ensembl Regulatory Build" which is another option in the "group:" selection, where you could output the "hub_20163_RegBuildOverview" table and get results. You can click the "describe table schema" button in the Table Browser to learn what the fields are for the data you are acquiring.

Here is the Browsing session for the above session (pointed to the hgTracks CGI instead of hgTables CGI): http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=mm10_regulatory_build

If you scroll down you will see how the "Ensembl Regulatory Build" hub has many interesting levels of track data to explore on mm10.

Of last note, you may want to also look at resources like the ENCODE project to see data on mm10 related to TF binding sites, promoters, enhancers, and silencers. They have a SCREEN site, which is a web-based search and visualization engine specifically designed for the Registry of candidate Regulatory elements:
https://www.encodeproject.org/data/annotations/
http://screen.encodeproject.org/

Thank you again for your inquiry and for using the UCSC Genome Browser. If you have any further questions and reply to gen...@soe.ucsc.edu messages will be 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
UC Santa Cruz Genomics Institute

Training videos & resources: http://genome.ucsc.edu/training/index.html

Want to share the Browser with colleagues?
Host a workshop: http://bit.ly/ucscTraining

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CY4PR02MB285441C81BDC7FBD73E1433DD5D80%40CY4PR02MB2854.namprd02.prod.outlook.com.