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Question: total number of unique transcription factors in MotifDB
0
12 months 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.

modified 12 months ago by Paul Shannon360 • written 12 months ago by scotronq0
1
12 months 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