Visualizing Genomic Interactions
5
5
Entering edit mode
8.4 years ago
sah9b ▴ 100

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!

genomics visualization • 6.8k views
ADD COMMENT
3
Entering edit mode
8.4 years ago
Ryan Dale 4.9k

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.

ADD COMMENT
2
Entering edit mode
8.4 years ago
Ido Tamir 5.2k

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

ADD COMMENT
2
Entering edit mode
7.5 years ago
Lynxoid ▴ 220

WashU EpiGenome Browser has what you want.

ADD COMMENT
1
Entering edit mode
8.4 years ago

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

ADD COMMENT
1
Entering edit mode
8.4 years ago
biorepine ★ 1.5k

@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

ADD COMMENT

Login before adding your answer.

Traffic: 1229 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6