Visualizing Genomic Interactions

Question

[sah9b]

Hi,

I'm looking for a way to view genomic interactions data generated by ChIA-pet or chromosome conformation capture technologies. I'm not interested in circos plots or heat maps, I want an interactive genome browser solution. For an example of what I'm looking for check out the browser shots this paper: http://www.sciencedirect.com/science/article/pii/S0092867411015170

Thanks!

Answer 1

[Ryan Dale]

These ENCODE ChIA-PET tracks show signal as bigWig and the interactions in BED12 format (with darker colors indicating stronger evidence of interaction).

It's not exactly the "arcs" visualization in the paper, but it is an interactive solution that you can easily view in the context of the rest of ENCODE.

Answer 2

[Ido Tamir]

The savant genome browser has a mate-pair mode showing long distances with arcs.

http://genomesavant.com/savant/index.php

http://bioinformatics.oxfordjournals.org/content/26/16/1938/F2.expansion.html

you might be able to feed other data into it that then gets displayed with arcs

Answer 3

[Lynxoid]

WashU EpiGenome Browser has what you want.

Answer 4

[Alex Reynolds]

You might contact the Stamatoyannopoulos lab about 5C diagrams. Take a look at Fig. 5 in this recent Nature paper.

Answer 5

[biorepine]

@Alex: I think they were drawn using illustrator or others @Sah9b: They used CHIA-PET Browser (still in development) to produce the figures in cell paper.

http://cms1.gis.a-star.edu.sg/index.php

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872882/

HTH R