Hi, I'll be doing RNA-seq in the near future and need to know how can I search for a consensus sequence in the promoter of the genes that are differentially expressed. I'm interested in figuring it out if the genes that are differentially expressed are regulated by two specific transcription factors. One way to narrow down the candidates would be to look for the consensus sequence of the response elements of the transcription factors in the promoter of the genes. There are reports in the literature of the response elements consensus sequences, but I don't know what software to use to investigate if my genes have those motifs. Thank you.
Extract your promoters' sequences to FASTA files and run them through MEME to discover putative motifs. You can then use the MEME result with TOMTOM to compare those putative motifs with known TF consensus sequences. The highest-ranking matches are probably of interest.
Another approach is to run the command-line version of FIMO against Jaspar, TRANSFAC and other TF databases not available through the web interface to do a whole-genome scan for putative TF binding sites at a few different statistical thresholds.
Once you have a whole-genome scan or two in hand, you can use set operations with BEDOPS
bedmap to map promoters or other regions of interest from your differential analysis to the TF binding sites in that whole-genome scan, to retrieve their names, positions, and other metadata.
HOMER may be another useful tool for motif discovery, as well, which I've seen mentioned from time to time.
GimmeMotifs is another resource that may be of use, which may be a little more user-friendly, though the documentation suggests that it doesn't give as much control over search parameters as the MEME suite.