[Bioc-devel] ¿A useful addition to MotifDb package?

[Steve Lianoglou]

Cool!

Thanks for the update,
-steve

On Wed, Nov 7, 2012 at 5:40 PM, Paul Shannon <pshannon at fhcrc.org> wrote:
> Hi Steve and all,
>
> MotifDb 1.1.6 (devel) now includes the transcription factor binding motifs from the stamlab footprints suggested by Steve.   Thanks for that tip, Steve.
>
> The new motifs are not associated with their binding protein, as all the others motifs in MotifDb are: that information was not supplied by the stamlab.  Instead, each motif
> is annotated as 'known' or 'novel'.  That information is recorded in the the metadata for the those 683 new motifs in MotifDb.
>
> Here is the result of the show method:
>
>> library(MotifDb)
>> MotifDb
>
> MotifDb object of length 2769
> | Created from downloaded public sources: 2012-Nov-01
> | 2769 position frequency matrices from 6 sources:
> |    FlyFactorSurvey:  614
> |               hPDI:  437
> |        JASPAR_CORE:  459
> |             ScerTF:  196
> |            stamlab:  683
> |           UniPROBE:  380
> | 22 organism/s
> |           Hsapiens: 1188
> |      Dmelanogaster:  739
> |        Scerevisiae:  464
> |          Mmusculus:  329
> |        Rnorvegicus:    8
> |           Celegans:    7
> |              other:   34
> Dmelanogaster-FlyFactorSurvey-ab_SANGER_10_FBgn0259750
> Dmelanogaster-FlyFactorSurvey-ab_SOLEXA_5_FBgn0259750
> Dmelanogaster-FlyFactorSurvey-Abd.A_FlyReg_FBgn0000014
> Dmelanogaster-FlyFactorSurvey-Abd.B_FlyReg_FBgn0000015
> Dmelanogaster-FlyFactorSurvey-AbdA_Cell_FBgn0000014
> ...
> Mmusculus-UniPROBE-Zfp740.UP00022
> Mmusculus-UniPROBE-Zic1.UP00102
> Mmusculus-UniPROBE-Zic2.UP00057
> Mmusculus-UniPROBE-Zic3.UP00006
> Mmusculus-UniPROBE-Zscan4.UP00026
>
>  - Paul
>
> On Oct 9, 2012, at 7:53 AM, Steve Lianoglou wrote:
>
>> Hi Paul + devs,
>>
>> Alex Reynolds's answer to this biostar post:
>> http://www.biostars.org/post/show/54511
>>
>> Lead me to this paper:
>> http://www.sciencedirect.com/science/article/pii/S0092867412006393
>>
>> and this dataset:
>> ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/footprints/README
>>
>> Which made me write this email.
>>
>> -steve
>>
>> --
>> Steve Lianoglou
>> Graduate Student: Computational Systems Biology
>> | Memorial Sloan-Kettering Cancer Center
>> | Weill Medical College of Cornell University
>> Contact Info: http://cbio.mskcc.org/~lianos/contact
>



-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact