[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
>>>>>>
>>>>>>
>>>>
>>>> *TODAY*/(Beta) /*.*Powered by Yahoo!
>>>>
>>>> Armored catfish wreak havoc in U.S. South
>>>>
>>>> <http://news.yahoo.com/blogs/sideshow/armored-catfish-wreaking-havoc-south-
>>>> florida-lakes-182812663.html;_ylc=X3oDMTFia2oyNjZoBF9TAzk1NDAxMDAyNwRwa2cDa
>>>> WQtMjIzODM5NARzeWlkA2RfZWNoMGQ4MGQ-#more-4190>
>>>>
>>>> Privacy Policy
>>>> <http://info.yahoo.com/privacy/us/yahoo/webbeacons/details.html>
>>>>
>>>> [[alternative HTML version deleted]]
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at r-project.org<mailto:Bioconductor at r-project.org>
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> /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>
>>>
>>
>> [[alternative HTML version deleted]]
>>
>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
More information about the Bioconductor
mailing list