Question: finding consensus TF binding sites in a list of genes
gravatar for Victoria
12 months ago by
Victoria0 wrote:

Hi everyone,

I am working on a transcription factor and performed RNA-Seq to find the possible targets for it. Now I want to know if the DEGs are bound by the TF directly or not. So I am looking for the consensus DNA binding sites in the promoter regions of the DEGs. Could anyone suggest an online database that I can find if there are DNA binding sites within my gene list? The results do not necessarily need to be confirmed by ChIP-Seq; because I checked and there is very few genes found to be the target of this TF by ChIP-Seq. I am looking for predicted binding sites (PWMs).


ADD COMMENTlink written 12 months ago by Victoria0

could be good to know what organism are you analysing

ADD REPLYlink modified 12 months ago • written 12 months ago by JC11k

The data is in human. Actually I used Transfac. The thing is that I find tons of PWM sites and am not sure how I should use them in my analysis. Almost all of my DEGs have a PWM for the TF in their promoter sequence. Also, I used MotifMap to find the target genes, there I find less than 100 genes (I know it is not complete based on the papers I have read. If you could suggest me online databases or some publications that have used them, it can be very helpful in my research. Thanks

ADD REPLYlink modified 12 months ago • written 12 months ago by Victoria0

ADD REPLYlink written 12 months ago by shoujun.gu310
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