Dear All,
Based on ORCA conserved regions, CpG islands, and histone methylation, I predict a putative promotor for my gene of interest with one of my colleague's help. I need to find/predict which transcription factors are binding to this region. How can I do that? Is there any available free software/ webware that I can use to find them based on the sequence?
I would like to have a list of transcription factors, so I can prove them experimentally.
Thank you
Chamara
If you are working on human genome. UCSC genome browser is a good place to go.
1) open UCSC genome browser (https://genome.ucsc.edu/index.html)
2) Turn on the "TFBS Conserved" track
3) input the genomic coordinate of the promoter to look up all the potential transcription factor binding sites that are conserved between human, mouse and rat.
If you are working on other genomes. Use FIMO (http://meme-suite.org/doc/fimo.html）
Hello, you can use the Remap catalog. Find below the link towards the catalog. Use the annotation tool to state the genomic coordinate of your promoter (bed file) , and you will get the list of the transcription factors binding the promoter.
http://pedagogix-tagc.univ-mrs.fr/remap/
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