JASPAR, TFs and their target genes

Question

[ilyco]

Hi, I have began using the BioConductor package TFBSTools to search through the JASPAR 2014 database. However, the instructions are rather vague regarding the available options. I would like to obtain a list of transcription factors for mouse and their preferred binding sites.

I am trying to analyse a set of genes by obtaining the set of transcription factors that possible target them. For this, I have retrieved their promoter sequences using the biomaRt package and I was hoping I could search each promoter site for possible transcription factors that could bind to it. I have searched for smart ways of doing this rather than a brute force approach, but was unable to find anything specific.

Regardless, even for the brute force approach, I am unsure how to retrieve the list of transcription factors for mouse from JASPAR and their preferred binding sites (PWM matrices or anything).

Any help regarding this matter would be appreciated.

Thank you!

Answer 1

[micahgearhart]

Check out MotifDb. Something like query(MotifDb, 'Mmusculus') should return the list you want.

This code will work for one gene and one promoter for Drosophila:

txdb <- makeTranscriptDbFromBiomart(biomart="ensembl",dataset="dmelanogaster_gene_ensembl")
tx <- transcriptsBy(txdb, by = "gene")
myDNA<-getPromoterSeq(tx["FBgn00123456"], Dmelanogaster, upstream = 2500, downstream = 500)
motif <-round(100*query(MotifDb,"esr1")[[1]])
matchPWM(motif, myDNA[[1]][[1]], "70%")

-Micah

[ilyco]

Thank you!

Answer 2

[Alex Reynolds]

FIMO will use your TF PWMs and search for binding sites across your genome of interest. Once you have those sites, you could use a tool like bedmap to map them to a set of promoter regions.

[ilyco]

Thank you! I will try it out.