tfbsConsSites

[Clayton Kenneth Collings]

Hello,

I was wondering if CTCF was included in the ‘tfbsConsSites' table.

I don’t see it.  If it is, what is the name?

I did an analysis using  computationally predicted CTCF sites from a different source, 

but I also did an genome-wide analysis surrounding these tfbsConsSites and need to know if CTCF is included.

http://ucscbrowser.genap.ca/cgi-bin/hgTables?hgsid=213993_qIcXI6SyNhqV1qBESrQyMiXkifvT&hgta_doSchemaDb=hg19&hgta_doSchemaTable=tfbsConsSites

Thanks for your time.

Sincerely,

Clayton

Clayton K. Collings, PhD

Bioinformatics Analyst

Shilatifard Laboratory

Department of Biochemistry and Molecular Genetics

Northwestern University Feinberg School of Medicine

Robert H. Lurie NCI Comprehensive Cancer Center

http://www.feinberg.northwestern.edu/sites/biochem/

 

Searle 6-469

320 E. Superior St.

Chicago, IL  60611

Educate, Discover, Improve Health 

[Cath Tyner]

Hello Clayton,

Thanks for using the UCSC Genome Browser and for inquiring about the table location for CTCF binding sites. 

​Here is a ​related 

previously answered mailing list question

​.​

From the description page for tfbsConsSites

​, ​u

nder the methods section:
The Transfac Matrix Database (v.7.0) contains position-weight matrices for 398 transcription factor binding sites, as characterized through experimental results in the scientific literature. Only binding matrices for known transcription factors in human, mouse, or rat were used for this track (258 of the 398).

If a factor isn't in our list of 258, it did not meet our criteria

​ for inclusion in th

e

​ ​

tfbsConsSites table

​.​

Under the credits section, you can see that "these data were generated using the Transfac Matrix and Factor databases created by Biobase."

You can search for any of the 398 full data set of factors on the Transfac site from Biobase

​​ on their transfac database.

Searching

​ the​

Transfac

​ database​

for "factor name" does yield 4 results, including the result for human

​.​

For future reference, ​t

here are many other UCSC Genome Browser tables that reference CTCF, for example:

Transcription Factor ChIP-seq track
This track shows CTCF binding sites from a large collection of ChIP-seq experiments.
In the table wgEncodeRegTfbsClusteredV3, you can filter for "CTCF" in the "name" column.

You can also go to the hg19 browser

​ ​

and click on the "track search" button to search for "CTCF."

Please respond to this list if you have further questions!

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

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​Enjoy,​

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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