Question: 4DGenome or another comprehensive database of chromatin interactions
1
gravatar for Adam Przedniczek
2.8 years ago by
Poland / Warsaw
Adam Przedniczek30 wrote:

I'm searching for the most comprehensive source of chromatin interactions to support enhancer targets (data such like Hi-C, ChIA-PET, IM-PET, 5C, 4C, 3C, etc.) and my question according that could be split into two following parts:

  1. On page http://epigenie.com/epigenetic-tools-and-databases/ I've found out links to two databases, but the reference to 4D Genome doesn't work. Does anybody know whether this database http://4dgenome.int-med.uiowa.edu was moved somewhere else or maybe its only internally available for U Iowa community? (I'm asking about probably exclusive access, because on Tan's lab page http://www.healthcare.uiowa.edu/labs/tan/software.html only the 4DGenome has the trailing part of the link int-med.uiowa.edu (presumably this int-med strands for internal/general medicine or maybe in the sense of internal/intranet access), whereas all other services like IM-PET has its link starting with http://www.healthcare.uiowa.edu/labs/tan/.

  2. Maybe you know even better database for chromatin interactions covering as much as possible cell lines/tissue types for GRCh38 assembly or any other whose coordinates could be easily converted, e.g. by liftOver? I need data only for human and mouse, but I would be grateful also for solely human data.

Thank you in advance for your answer.

3c 4c conformation 5c hi-c • 973 views
ADD COMMENTlink modified 2.8 years ago by Giovanni M Dall'Olio26k • written 2.8 years ago by Adam Przedniczek30

Perhaps it's worthwhile contacting the corresponding author of the 4DGenome paper, Kai Tan and ask for its whereabouts? The 3CDB with curated 3C (only) data listed in EpiGenie could be helpful. I think this sort of data will be available in Ensembl in the (near?) future. For the time being, there is a prototype display for cis-regulatory interactions. Check Daniel's post on the Ensembl blog.

ADD REPLYlink written 2.8 years ago by Denise - Open Targets4.8k
2
gravatar for Adam Przedniczek
2.8 years ago by
Poland / Warsaw
Adam Przedniczek30 wrote:

This problem has been finally solved with help from prof. Kai Tan. It occurred that his lab has been moved from University of Iowa to Children's Hopspital of Philadelphia, so has been this service. Now, the working link is: http://4dgenome.research.chop.edu

ADD COMMENTlink written 2.8 years ago by Adam Przedniczek30
1
gravatar for Giovanni M Dall'Olio
2.8 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

The ENCODE project also provides data on 3D interactions.

Have a look at the ENCODE data portal, and on the "Assay" list on the left, select the techniques you are interested in:

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Giovanni M Dall'Olio26k
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