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Question: total number of unique transcription factors in MotifDB
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gravatar for scotronq
4 weeks ago by
scotronq0
scotronq0 wrote:

I have been using your MotifDB software. I am curious how many unique transcription factors are in your updated database. Thank you for your time.

ADD COMMENTlink modified 4 weeks ago by Paul Shannon360 • written 4 weeks ago by scotronq0
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gravatar for Paul Shannon
4 weeks ago by
Paul Shannon360
Paul Shannon360 wrote:

Hi Scott,

As a preface to my answer: we have added three new methods to the new release of MotifDb:

  1. geneToMotif
  2. motifToGene
  3. associateTranscriptionFactors

All three require a "source" argument, either "MotifDb" or "TFClass" - thus offering two data sources for the sometimes imprecise business of linking a motif to its cognate transcription factor/s.  TFClass is a liberal source based on the 2015 paper https://www.ncbi.nlm.nih.gov/pubmed/25361979;  multiple TFs are associated with many motifs.  The MotifDb source is more conservative, typically associating just one TF with each motif.   

For either the old (1.18) or new release of MotifDb, you can answer your question with this approach show below. Note that these counts use only metadata held directly in MotifDb itself, obtained from the providers, and is thus equivalent to the conservative source="MotifDb" approach described above.

 length(unique(mcols(MotifDb)$geneSymbol))  # [1] 3012
 length(unique(mcols(query(MotifDb, "hsapiens"))$geneSymbol)) # [1] 1273

 jaspar.2016.human.motifs <- query(query(MotifDb, "hsapiens"), "jaspar2016")
 length(unique(mcols(jaspar.2016.human.motifs)$geneSymbol)) # [1] 389

- Paul

 

ADD COMMENTlink written 4 weeks ago by Paul Shannon360
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