finding consensus TF binding sites in a list of genes

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4.6 years ago

Victoria ▴ 10

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,

TF binding site online databases • 1.1k views

ADD COMMENT • link 4.6 years ago by Victoria ▴ 10

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could be good to know what organism are you analysing

ADD REPLY • link 4.6 years ago by JC 13k

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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