Visualization tools for 3C/Hi-C long-range interaction data?

Question

I have identified a genomic region (CpG island) that is enriched for a characteristic of interest in the vast majority of my samples.

After viewing it in the UCSC genome browser, I have confirmed that it does not overlap any annotated gene promoters, gene bodies, or retrotransposons, but am convinced that it is functionally interacting with something long range.

Is there a publicly available visualization tool where I can input my genomic region and get a list of topologically associated domains from 3C or other chromatin-chromatin interaction data?

What assembly is your genomic region of interest in? – juniper- Sep 18 '17 at 00:32 — juniper-, Sep 18 '17 at 00:32
The assembly I used was hg19/GRCh37 – Ben D. Sep 26 '17 at 18:00 — Ben D., Sep 26 '17 at 18:00

score 6 · Accepted Answer · answered Aug 27 '17 at 22:41

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I would also recommend two very recent Hi-C visualization frameworks (with some public data available in both): HiGlass and JuiceBox.

answered Aug 27 '17 at 22:41

golobor

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HiGlass has the result of 7 different TAD callers available. Example using hg38 can be found here: http://higlass.io/app/?config=IPCHmdOQR4CDY2sqj5VJHQ
Another example using hg19 is here: http://higlass.io/app/?config=OBa3x6FiQtSC5g8Mj6u0pQ

The TAD calls are from Forcato et al. 2017.
– juniper- Sep 18 '17 at 00:38

score 3 · Answer 2 · answered Nov 19 '17 at 20:42

If you have more than a dozen or even hundreds of regions that you want to compare you could check a companion tool of HiGlass called HiPiler. HiPiler lets you arrange, cluster, and pile up to thousands of genomic regions. Take a look at this 5min video introduction to see if the tool could help you to answer your questions.

Disclaimer: I am the creator of HiPiler.

score 2 · Answer 3 · answered Jul 21 '17 at 18:47

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Depending on the genome you want, you may be able to use the chorogeneome navigator, which is from some of my colleagues. This uses a number of public HiC datasets and allows you to view interactions.

answered Jul 21 '17 at 18:47

Devon Ryan

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Visualization tools for 3C/Hi-C long-range interaction data?

3 Answers3