How to check whether two genomic regions contact in 3D?

Question

[trulala]

Hello,

I want to check for a group of human genes in a specific cell type, whether they contact each other in 3D (based on published data such as Hi-C, 3C, 4C, etc). What is the simplest way to do this? Is there some browser to search for genomic coordinates? Did someone compile lists of genes contacting each other in a given cell type?

Thanks!

Answer 1

[TriS]

i think you are looking for the WashU browser here

there are also other answers Visualizing Genomic Interactions

[trulala]

The WashU browser works, thank you. However, it shows only neighboring genomic regions. How can I check whether two particular genes situated at different chromosomes contact each other in 3D?

[TriS]

hmmm...a laborious way (that however will give you an answer) would be to download the ChIAPET data, check whether your genes are within x kb  from the fragments, keep track of which fragment maps to which gene and see whether the fragments that are in contact map around your gene. you can use ChipSeeker to map regions to genes. I'm not aware otherwise of a browser that allows you to query for two genes and see if they are in contact

Answer 2

[Emily_Ensembl]

We're working on getting it into Ensembl. No idea of timescale or what it'll look like, but I'm very excited!

Answer 3

[Fidel]

Maybe the juicebox from Aiden Lab can help you. It was published as part of their comprehensive paper on Hi-C. I have not  tested the program but seems promising.

Answer 4

[trulala]

Is there available something like a table of genomic domain coordinates?

Or a table of genomic loop coordinates?

Answer 5

[encoder]

It depends on the cell type of interest. Most of the Hi-C papers will give the list of significant interactions they call as a supplement. Which cell type do you want to check the 3D interactions?