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

Zhu, Lihua (Julie) Julie.Zhu at umassmed.edu
Tue Apr 24 19:47:05 CEST 2012


Eloi,

I would like to use MotIV for a c.elegans dataset. What data source would
you recommend for matchMotif? Many thanks for your help!

Best regards,

Julie


On 4/24/12 1:28 PM, "Mercier Eloi" <emercier at chibi.ubc.ca> wrote:

> Hello,
> 
> I am one of the developer of MotIV. I will be happy to help you if you
> have any question regarding the package.
> 
> First, I want to mention that in the Plos One paper, we used PICS,
> rGADEM and MotIV as a pipeline but MotIV can be use as a stand alone.
> Some of the advanced functions won't be available though.
> 
> Since the PWMs in MotIV correspond to human TF, you may have to use your
> own list of PWMs. What MotIV needs is a simple list of matrices
> (head(jaspar) to view the format).
> Jaspar's PWMs can be easily downloaded but it seems it only contains ~20
> motifs. On the other hand, AthaMap has more motifs but I did not manage
> to find an easy way to get them. Another place to look at is the AGRIS
> website (http://arabidopsis.med.ohio-state.edu/downloads.html).
> 
> If you're only interested by the identification of the motifs and do not
> want to do further analysis with R, I recommend you to look at
> http://www.benoslab.pitt.edu/stamp for the identification of your motifs.
> 
> Regards,
> 
> Eloi Mercier
> 
> 
> On 12-04-24 07:36 AM, nooshin wrote:
>> Thanks a lot for your suggestion. I will for sure have a look and inform
>> you.
>> Bests,
>> Nooshin
>> 
>> 
>> On 04/24/2012 04:15 PM, Tim Triche, Jr. wrote:
>>> Ah, I see.  GSL is a useful library to have installed regardless.
>>>   Hope things work out.  I found your exchanges with Paul to be useful
>>> reading, but obviously I was not reading closely enough, since Paul
>>> started off his code sample with biocLite('MotIV').  Oops :-o
>>> 
>>> Here is a paper that I found interesting, which does go into some
>>> detail towards a "bulk" approach, from Gottardo's group:
>>> 
>>> http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0016432
> 
>>> Perhaps it will be useful to you as well, would be curious to hear if so.
>>> 
>>> --t
>>> 
>>> On Tue, Apr 24, 2012 at 7:00 AM, nooshin<n_omranian at yahoo.com
>>> <mailto:n_omranian at yahoo.com>>  wrote:
>>> 
>>> 
>>>      Thanks, it's been already solved, it needs GSL package, which is a
>>>      bit problematic, but I solved it already.
>>> 
>>>      But it does include only 5 matrices (in the webpage) for
>>>      arabidopsis and in the package also!
>>>      I'm downloading manually from AthaMap!
>>> 
>>>      Thanks again and keep waiting for 'bulk' approach.
>>> 
>>>      Bests,
>>>      Nooshin
>>> 
>>> 
>>>      On 04/24/2012 03:16 PM, Tim Triche, Jr. wrote:
>>>>      source("http://bioconductor.org/biocLite.R")
>>>>      biocLite("MotIV")
>>>> 
>>>>      ought to do the trick for you
>>>> 
>>>> 
>>>> 
>>>>      On Tue, Apr 24, 2012 at 1:01 AM, nooshin<n_omranian at yahoo.com
>>>>      <mailto:n_omranian at yahoo.com>>  wrote:
>>>> 
>>>> 
>>>>          Hi Paul,
>>>> 
>>>>          Thanks a lot.
>>>>          I forgot to include bioc, since I only replied to you (no to
>>>>          all).
>>>> 
>>>>          I can"t install MotIV package to check. I checked in google but I
>>>>          couldn't find any solution! Do you have any suggestion for
>>>>          installing
>>>>          this package?
>>>> 
>>>>          Bests,
>>>>          Nooshin
>>>> 
>>>>          On 04/23/2012 06:35 PM, Paul Shannon wrote:
>>>>>  (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
>>>>>> 
>>>>>> 
>>>> 
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>>>> 
>>>> 
>>>>      --
>>>>      /A model is a lie that helps you see the truth./
>>>>      /
>>>>      /
>>>>      Howard Skipper
>>>>      <http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
>>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> /A model is a lie that helps you see the truth./
>>> /
>>> /
>>> Howard Skipper
>>> <http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
>>> 
>> 
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