I am looking at TFBS analysis for a colleague. He is interested in TRANSFAC but it being commercial I am interested in JASPAR. From Wasserman and Sandelin 2004 paper (doi:10.1038/nrg1315) they state "recurrent alignment of the 5' edges of ESTs and/or full-length cDNAs can be indicative of promoter locations".
While this may seem obvious, it was written 'pre-NGS' and as such I am wondering what the current consensus is on this? It is hard to search the literature for these sorts of issues and no good reviews have jumped out. To be more specific I was thinking about work stemming from this: is it worth a capture-seq experiment on differentially expressed genes to look for promoters, TFBS or other regulatory sequence from the 5' 'edge', or can you use the rather ad hoc assertion made above?
Thoughts appreciated.
While this may seem obvious, it was written 'pre-NGS' and as such I am wondering what the current consensus is on this? It is hard to search the literature for these sorts of issues and no good reviews have jumped out. To be more specific I was thinking about work stemming from this: is it worth a capture-seq experiment on differentially expressed genes to look for promoters, TFBS or other regulatory sequence from the 5' 'edge', or can you use the rather ad hoc assertion made above?
Thoughts appreciated.
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