[BioC] from TF DNA binding motif to downstream genes?

Paul Shannon pshannon at systemsbiology.org
Fri Jan 15 01:44:59 CET 2010

Can I get advice from on good ways to find genes -- perhaps with a high false-positive rate -- whose promoters contain known DNA binding motifs?

Hu et al, "Profiling the Human Protein-DNA Interactome Reveals ERK2 as a Transcriptional Repressor of Interferon Signaling" identifies

   17,718 PDIs [protein-DNA interactions] between 460 DNA motifs predicted to regulate 
   transcription and 4,191 human proteins of various functional classes.

I wish to take those 460 motifs -- many of them only 7 bases long -- and find the genes whose transcription they control.

I suspect the answer lies in some artful use of Biostrings, BSgenome (which together provide efficient genome search), along with annotation to find the transcription start site of  known genes.   But before I start, I think it prudent to get the advice of those who may know more than me.


 - Paul

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