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Question: question on MotifDb package
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gravatar for Paul Shannon
3.7 years ago by
Paul Shannon360
Paul Shannon360 wrote:
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
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