tool to find enhancer associated to gene list

Question

[Chironex]

Hi guys, i'm searching for a way to find, given a list of genes, the associated encode enhancers. I want something similar to Genehancer, https://academic.oup.com/database/article/doi/10.1093/database/bax028/3737828, but it works with human and I need mouse. thank u

[ATpoint]

There is no gold standard resource that in a bullet-proof fashion connects enhancers to genes. What you can find are these "enhancer databases" as suggested already, and then you have to do the matching, either by proximity or other metrics. Enhancer-gene connections are imo one of the most unsolved problems in biology since there is very little high-throughput gold standards to do that.

• Any methods that connect them by proximity or other features are sort of arbitrary or indirect.
• HiC datasets allow (to some extend depending on resolution) to connect loci, but HiC is still rate, and these connections are celltype and probably treatment-specific, so this does not always help.
• targeted capture-C datasets are even more rare.
• Existing databases do not always cover the celltypes you need, plus don't respect treatment effects and the exact situation your cells are into

It's really a mess.

Answer 1

[bk11]

You can check out EnhancerAtlas 2.0.

[Chironex]

Hi, Ia am sorry, I forgot to specify that I would use ENCODE ENHANCERS. I've found screen project. https://screen.encodeproject.org/index/cversions But I need to put a list of genes instead checking one by one, so I'm trying to manage it. Thank you anyway