Could anyone share their experience on using Transfac professional? Could this comercial database be substituted by other public dataset ( e.g. Jaspar and recent Encode Chip-Seq Data).
I am interested in analyzing promoter sequences (of 200 genes) and searching for possible TF. Recently our lab get a small funding. Just wondering whether it worth the investment of 10,000 Dollars.
Any comments is highly appreciated,
4 answers
You have available a lot of public databases that are really well done and free. You should use:
- Jaspar (http://jaspar.genereg.net/)
- UniProbe (http://the_brain.bwh.harvard.edu/uniprobe/index.php)
- HOCOMOCO (http://autosome.ru/HOCOMOCO/)
- Taipale paper (doi: 10.1016/j.cell.2012.12.009)
Can you tell us the differences for Jaspar, UniProbe and HOCOMOCO? And which is more precise?
Jaspar is mainly based on SELEX experiments. It is highly reliable even though it is starting to get old. We are currently working on a new version. UniProbe is based on protein microarray data. HOCOMOCO is mainly based on ChIP-seq data. They are all nice and most of all very complementary.
Thank you! It's useful!
I think you should evaluate the value you get from TRANSFAC compared to the open access tools.
For upstream TF search you can utilize extensive list of tools provided by MEME Suite.
If you are interested in TF enrichment you can try the curated resource ChIP-Seq data: ChEA
An other extremely nice tool for TF enrichment analysis using ChIP-seq it the peak-motif analysis tool of RSAT at http://rsat.ulb.ac.be/index.html.
Genexplain recently uploaded a white paper explaining the difference between TRANSFAC and JASPAR. It seems when we use TRANSFAC there are chances that we don't miss important matrices that play a role in regulation of gene of interest. The white paper link can be found here:
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I have been a Transfac user for more than an year now. Initially I did have a little trouble understanding it, but I feel they have done a good job lately and made it much more user friendly. Plus now it comes upstream analysis capabilities (they were not there initially), which makes it a more complete platform. Of course there is the price issue when compared with the free databases, but I feel (atleast for my work) its more reliable and more complete.