[BioC] question on MotifDb package

Paul Shannon paul.thurmond.shannon at gmail.com
Tue Mar 11 16:58:58 CET 2014

Hi William,

You are correct:  the stamlab transcription factor binding motifs in MotifDb are not from their 2012 Cell paper (pmid 22959076) but from the Nature paper published at the same time (pmid 22955618):

  "An expansive human regulatory lexicon encoded in transcription factor footprints."  

This is corrected in bioc-devel, and will be in the release coming up soon.   I hope, too, to include all of the motif/TF gene mappings alluded to in the paper:

   A total of 394 of the 683 (58%) de novo motifs matched 
   distinct experimentally grounded motif models, accounting 
   collectively for 90% of all unique entries across the 
   three databases [TRANSFAC, JASPAR, UniPROBE).

 - Paul

On Mar 10, 2014, at 6:45 PM, "Swindell, William" <wswindel at med.umich.edu> wrote:

> Dear Paul Shannon,
> Sorry to bug you, but I had a question concerning the MotifDB R package:
> http://bioconductor.org/packages/release/bioc/html/MotifDb.html
> The help files describe the following motif sources:
> FlyFactorSurvey:  614 
> hPDI:  437 
> JASPAR_CORE:  459 
> jolma2013:  843 
> ScerTF:  196 
> stamlab:  683 
> UniPROBE:  380
> For the 683 stamlab motifs, I think the cited reference is:
> Neph S, Stergachis AB, Reynolds A, Sandstrom R, Borenstein E, Stamatoyannopoulos JA. Circuitry and dynamics of human transcription factor regulatory networks. Cell. 2012 Sep 14;150(6):1274-86.
> Do the 683 motifs come from a supplemental data file for this paper? If so, I couldn't find it...that paper doesn't seem to derive new motifs at all...it just includes some analyses using motifs from TRANSFAC. Thus I am confused regarding where the 683 "stamlab" motifs comes from. Thanks for any help you can provide.
> Best regards,
> William Swindell
> University of Michigan, Dermatology
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

More information about the Bioconductor mailing list