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

[Paul Shannon]

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