Question: How to obtain predicted or lab-verified TFBS in UCSC Genome Browser?
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gravatar for allyson1115ar
3.8 years ago by
allyson1115ar20 wrote:

I would like to obtain 2 data (any transcription factor will do) that have predicted or lab-verified transcription factor binding sites from UCSC genome browser. In Table Browser, I chose Regulation in the Group option and TFBS Conserved for Track. In the identifiers (names/accessions) part, I would like to know which identifier can return me more than 2000 sequences? 

Can anyone help me?

 

ucsc tfbs gene • 3.2k views
ADD COMMENTlink modified 3.8 years ago by Maximilian Haeussler1.3k • written 3.8 years ago by allyson1115ar20
1
gravatar for Maximilian Haeussler
3.8 years ago by
UCSC
Maximilian Haeussler1.3k wrote:

You can also download the mysql table tfbsConsSites from http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ or connect directly to the UCSC mysql server and get the table from there http://genome.ucsc.edu/goldenpath/help/mysql.html

ADD COMMENTlink written 3.8 years ago by Maximilian Haeussler1.3k
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gravatar for Anima Mundi
3.8 years ago by
Anima Mundi2.4k
Italy
Anima Mundi2.4k wrote:

Hello,

if you want to retrieve all TFBSs from the TFBS Conserved track you basically do not need to put any identifier. Just go to "get output", choosing e.g. "sequence" as output format. You can extend, if you like, your TFBSs in the following menu.

ADD COMMENTlink written 3.8 years ago by Anima Mundi2.4k
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