Question: JASPAR motifs download
1
gravatar for bharata1803
2.8 years ago by
bharata1803420
Japan
bharata1803420 wrote:

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?

ADD COMMENTlink written 2.8 years ago by bharata1803420
1

Hi, to dowload JASPAR matrices, go here (e.g. this one).

ADD REPLYlink written 2.8 years ago by Anima Mundi2.4k

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?

ADD REPLYlink written 2.8 years ago by bharata1803420

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.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Anima Mundi2.4k
1

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/

ADD REPLYlink written 17 months ago by asntech50

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.

ADD REPLYlink written 2.4 years ago by Kurban170
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 763 users visited in the last hour