Tf Names In Motifdb

Question

[liu4gre]

I am using MotifDb to have a look at the PWM of TFs. However there are some items named as "UW.Motif.0001". Would you mind tell me what it means? How can I convert it to TF?

Answer 1

[vj]

Many of the motifs' metadata are incomplete and you can get them by

mdb = query (MotifDb, 'UW.Motif.0001')
values(mdb) -> x
x$geneSymbol
# Convert to dataframe if you want
as.data.frame(x) -> dfx

[liu4gre]

Thanks. But I tried the command, and I get all the geneSymbol for UW.Motif are NA. Is there anything wrong?

[vj]

As I had mentioned earlier, the database seem to not have a TF geneSymbol mapping for that motif. If you try

mdb=query(MotifDb, 'hsapiens') 
values(mdb)

the output will show that some rows will have geneSymbols mapped to the motifs while others do not.

So in short, if you are looking specifically for UW.Motifs then you may have to write to either MotifDb or the people who provided the motifs.

Another way is probably to search all the known and annotated motif databases and try to find the closest known motifs. You can use tools like TOMTOM to do it for you. For that you have to export your motif(s) in a compatible format. I guess meme format should work (I have not tried it) and here is the code.

export(mdb[1], con="motif.meme", 'meme')

Or you could use MotIV::motifMatch to do it as well. You can get a crash course on how to do that here at the overview manual.

Hope this helps.