Dear Biostars community,
I am working with ChIP-seq and RNA-seq data of a TF. I know where the TF is binding and I know which genes are upregulated or downregulated upon loss of the TF. I would like to assign as accurately as possible the genes which are regulated by the putative enhancers. I have used tools like GREAT or BETA for this assignment. But I wondered if the bioinformatics community have released any more recent tools that are more accurate, perhaps by the use of machine learning.
¿Does anyone know good tools for enhancer-gene association predictions besides GREAT or BETA? ¿Is there any tool that uses machine learning for this purpose?
Best
Alejandro
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written
by
alejandrocastillaibeas •
1 answer
I wanted to recommend maybe GENIE3 or decoupleR, but they don't really do what you ask.
A more simplistic approach such as overlap with ENCODE candidate regulatory elements for your tissue/cell type of interest if available may be worthwhile. They have cRE-gene links, cRE locations, etc.
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