promoter analysis with DEG RNA-seq

Question

[m.esmaeilpour]

Hello. Please, does anyone introduce a websites that are active and do promoter analysis and transcription factor binding sites? My input data is a list of DEG from RNA seq data. Thanks

Answer 1

[Asaf]

The classic is MEME. It's input is the promoter sequences of your genes (you can get them using ucsc table browser for instance).

Motif finding is a nice concept in theory but I never saw a real world example in which it actually worked (aside from bacteria maybe)