Database For Transcription Factor Binding Sites Annotation (Tfbs)

Question

[J.F.Jiang]

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!

Answer 1

[Mary]

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.

[J.F.Jiang]

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?

Answer 2

[Gjain]

Hi,

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

• TRANSFAC Matrix models
• One important point to know is that not all the matrix models are experimentally curated or good. So not all models can be used from TRANSFAC.
• JASPAR is another one mentioned above with high quality matrix models.
• UniPROBE
• Human Protein-DNA Interactome (hPDI)
• Factorbook

hope this helps.

[J.F.Jiang]

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).

[Gjain]

please read Neilfws comment.

Answer 3

[Neilfws]

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.

[J.F.Jiang]

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!

[Neilfws]

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).

[J.F.Jiang]

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?