Question: Database For Transcription Factor Binding Sites Annotation (Tfbs)
3
gravatar for J.F.Jiang
7.6 years ago by
J.F.Jiang750
China
J.F.Jiang750 wrote:

hi,

I have looked into Yale TFBS in UCSC, but it seems that the TFBS in UCSC are not quite enough for me to overlap my snp positions.

Is there any database for transcription factor binding sites annotation (TFBS). Both the experimental data predict one are OK.

Thanks for these help! Annother question is that the UCSC Yale TFBS track has many results for different cells with same transfactors, while results of each cell do not contain all TFs in this track. So if i want to verify whether my snp is overlaped in this TFBS, can i combine all the results from different cells? If not, how can i handle this case, which make me much confused these days!

ADD COMMENTlink modified 7.4 years ago by Gjain5.3k • written 7.6 years ago by J.F.Jiang750
3
gravatar for Mary
7.6 years ago by
Mary11k
Boston MA area
Mary11k wrote:

ORegAnno has some you might be interested in. http://www.oreganno.org/ There's also an ORegAnno track at UCSC.

There's also the TFBS Conserved track at UCSC. It's predictions, and had some constraints about the ones that are reported (based on species conservation), but you might find some utility there too.

ADD COMMENTlink written 7.6 years ago by Mary11k

Thanks for your suggestion. The ORegAnno is a great databse. It indeed has some important information. But it seems that the result of this database has a large differences with UCSC, in which only 3-4 tf binding sites are displayed. So my question is that can i combine the results of these databases? It seems not. So which database is better for SNP TFBS overlap?

ADD REPLYlink written 7.6 years ago by J.F.Jiang750
3
gravatar for Gjain
7.6 years ago by
Gjain5.3k
Munich, Germany
Gjain5.3k wrote:

Hi,

here are the number of TBFs that have matrix models associated with it.

hope this helps.

ADD COMMENTlink written 7.6 years ago by Gjain5.3k

Thank you for your suggestions. But we do not buy the TRANSFAC database while the public version only offers few data for TFBS. And it seems that both the other three sources do not give the annotation of the TFBS (start and end).

ADD REPLYlink written 7.6 years ago by J.F.Jiang750

please read Neilfws comment.

ADD REPLYlink written 7.6 years ago by Gjain5.3k
2
gravatar for Neilfws
7.6 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

Yes, there are lots of such databases. I hate to answer with the words "try a Google search" but in this case...try a Google search for "transcription factor binding sites database". One of the most useful is the top hit: JASPAR.

ADD COMMENTlink written 7.6 years ago by Neilfws48k

The JASPAR is a very useful database. But it seems that the database offer us a matrix data for the transcription without giving the start and end annotations of the TFBS of the protein!

ADD REPLYlink written 7.6 years ago by J.F.Jiang750

You're quite right. I guess you could map to chromosomes yourself, by scanning them with the matrices. Or else there are other services which use JASPAR data: e.g. MAPPER database (http://genome.ufl.edu/mapper/) and oPOSSUM (http://www.cisreg.ca/oPOSSUM2_dev/help.html).

ADD REPLYlink written 7.6 years ago by Neilfws48k

Thanks for comment. It looks like that the mapper database is something like MATCH (using transfac matrix) software. Then is there any different between the two methods?

ADD REPLYlink written 7.6 years ago by J.F.Jiang750
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