Dear all,
my goal is to compare transcription factor binding sites (TFBS) across two species.
So what i've done so far was:
* extracting promoters from a set of (lets say) 100 genes of a specific biological pathway of species A and their orthologs in species B
* extract curated TFBS (in the form of PWM)
* mapped TFBS to promoter sequences of species A and species B with FIMO
* filtered the FIMO output for stringent q-values
Now, i would like to find a way to compare those TFBS across those 2 species to give relevant information about TF family different binding and highlight potential evolutionary insights about the biological pathway i'm studying. What do you suggest to do?
Maybe, for each gene, concatenate each specific TFBS hit and align them with the respective concatenated hits for the same TFBS of the ortholog(s) and calculate a diversity statistics like Pi, theta, Tajima'D can be a good option? in this case i would then calculate the average diversity value across all alignments for each TF family .
Additional question (and thanks for your time!):
A part promoters, do you recommend an alternative/better way to do (structural) diversity analyses for a specific biological pathway (say those 100 genes) across 2 species? Please feel free to shot them here. Brainstorming is needed.
thanks in advance for any opinion
