[BioC] Motif search -- access to JASPAR, MotIV package, more TF-PWM relationships?

[Paul Shannon]

(redirecting this back to the Bioc list…)

Hi Nooshin,

The 'bulk' approach is not quite so ready as I predicted.  I might have something by the end of the week.

As for mapping between PWMs and TFs, I have most often done this with 'tom-tom' from the meme website.  

But I just discovered what looks like a good -- maybe better -- approach:  the Bioconductor MotIV package, which includes a 2010 version of jasper.
Try this:

   source("http://bioconductor.org/biocLite.R")

biocLite ('MotIV')
library (MotIV); 
browseVignettes ('MotIV')

The jaspar data in this package has 130 TF-PWM mappings, which appear to be human.  More must be known, and publicly available.  The JASPAR website has a 'JASPAR CORE Plantae'  data set that 
   - is probably what you are interested in
   - might be downloadable, and convertible to the form MotIV wants.

Perhaps other readers of the list have other suggestions.

If you have any questions on this, please include 'BioC' in your reply, so that we can all get better at this!

 - Paul


On Apr 23, 2012, at 6:53 AM, nooshin wrote:

> 
> Hi Paul,
> 
> Many thanks for your comprehensive information and code!
> I have a question regarding to extract of PWMs. How and where I can download these matrices for all TFs that PWM is available for them? I need it only for Arabidopsis thaliana.
> Is there any package in R which I can give the TF and receive the PWM for it? Or any online database which I can download from it? I have a big problem since Friday to find out these matrices for different TFs of A.th. That would be so great if you can help me to get these matrices.
> 
>> If you want to do this in bulk, Herve' has some lovely code to make that efficient.
> Also can I have this? :)
> 
> 
> Thanks a lot in advance.
> Best regards,
> Nooshin
> 
>