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.