Question: finding consensus TF binding sites in a list of genes
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gravatar for Victoria
4 months ago by
Victoria0
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).

Thanks,

ADD COMMENTlink written 4 months ago by Victoria0

could be good to know what organism are you analysing

ADD REPLYlink modified 4 months ago • written 4 months ago by JC9.4k

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 4 months ago • written 4 months ago by Victoria0

http://homer.ucsd.edu/homer/motif/

ADD REPLYlink written 4 months ago by shoujun.gu280
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