Hello,
Currently, I want to make a list of Transcription factor-target gene pair. From this ensembl regulatory database I got the location of regulation region. From several databases, I also get a list of transcription factor genes,name of the genes and ensembl ID. My question right now is, how can I pair these 2 informations? I want to predict a transcription factor and its TFBS. If you have any suggestion how to predict a transcription factor gene (given the name/id) binds to a promoter region of a gene, please share with me. The output should be, a pair of TF gene and target gene, and coordinate where the TF will bind in the promoter region of the target gene.
I know about TF motifs like from JASPAR, but I can not download them. It is images. This is so confusing for me. Why would they provide an image? Is there any way to get this in a text file?
Hi, to dowload JASPAR matrices, go here (e.g. this one).
Thank you. I download the information from this link : pfm vertebrates. It seems all vertebrates data is there. Do you think for only homo sapiens is there?
You can select Homo sapiens by using its taxID, e.g. here.
Edit: the link for the human matrices just sends you to the homepage. To get the desired output, select the field "Species" and enter
9606.We now provide a REST API to get data from the latest release (2018) and also older releases of JASPAR http://jaspar.genereg.net/api/. Here is example to get matrices for Homo sapiens http://jaspar.genereg.net/api/v1/species/9606/
hi @bharata1803 did you finish your 'TF - target' file? if you did could you please share the way how you did that? because i have more than 800 animal TF sequences from ensembl, and i am also trying to find their target gene sequences.