Protocol Online logo
Top : New Forum Archives (2009-): : Bioinformatics and Biostatistics

how to find kappaB binding site on the promoter of a gene - kappaB binding site in gene promoter (Aug/18/2010 )

Dear fellows,

I am planning to do some experiment on the regulation of NF-kappaB subunit on some proinflammatory gene such as IL-8 and IL-6. I will do ChIP to see if NF-kappaB subunit such as p50 RelB bind on the promoter of IL-8 promoter. First of all I have to find the sequence of the binding site. I wanna know if there are any bioinformatic tools to do this job. thanks


If you can find a consensus binding sequence then you can search for that sequence in promoter regions of the genes. I think there is a site called TFbind or something similar that has a lot of the binding sites for transcription factors.


Yeah, Bob is right, and for NFkB there is a known consensus site which you can find in your promoters even manually