I have a list of genes that have been proven to be up-regulated in a human disease condition of interest. I also have a protein which according to literature is said to be a DNA binding protein. I wish to be able to computationally predict if the protein mentioned binds to any of the promoter sequences of my differentially expressed genes and if yes , then at which position?
Are there any Bioinformatic tools available for this task?
Dear Anchang Charles Gwellem
If you know the consensus sequence or the PWM of your DNA binding protein (a TF for example), you can use tools from the MEME suite or HOMER. If you don't, it will be difficult to predict anything, since informatics tools need minimal information to be efficient. In this case, you can perform EMSA assays with different probes to try to identify the binding sequence of your protein of interest. Good luck!
You need to know a bit about the protein. What is the DNA binding domain? Do you have an antibody for the protein? Antibodies can be used for Chromatin IP (ChIP) and the enriched DNA tested with primer pairs that walk along a promoter known to be responsive. If you do this for a few promoters you might find some consensus. Also, if you had a region of promoter sequence, you could do an in vitro footprint using recombinant DNA binding domain from your protein. This is a bit old school, but will get you the DNA sequence that your protein prefers.
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