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?
Database For Transcription Factor Binding Sites Annotation (Tfbs)
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!
3 answers
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.
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.
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).
Log in to answer this question.
More posts like this
-
Transcription factor binding sites using ATAC-seq peaks
written by courtnes •
-
Experimental method to count the mean number of DNA-bound transcription factors
written by Pascal •
-
How to obtain predicted or lab-verified TFBS in UCSC Genome Browser?
written by allyson1115ar •
-
RSAT: matrix scan result interpretation
written by dinesh •
-
How to find the binding sites for a particular transcription factor among the human genome
written by liuxiaomeng90 •
-
what does the transcription factor location tell me
written by Affan
-
More than PWMs for finding TFBS
written by ilyco •
-
Tools For Predicting Functional Effects Of Snps?
written by viavialin •
-
Questions About Snps Enrichment On Important Regulators In Ucsc
written by J.F.Jiang
-
Transcription Factor Binding Site Prediction
written by Panagiotis Alexiou •
