total number of unique transcription factors in MotifDB
Entering edit mode
scotronq • 0
Last seen 3.4 years ago

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.

motifdb • 577 views
Entering edit mode
Paul Shannon ▴ 460
Last seen 5 days ago
United States

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;  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



Login before adding your answer.

Traffic: 248 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6