The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data

Sarah B. Reiff, Andrew J. Schroeder, Koray Kırlı, Andrea Cosolo, Clara Bakker, Luisa Mercado, Soohyun Lee, Alexander D. Veit, Alexander K. Balashov, Carl Vitzthum, William Ronchetti, Kent M. Pitman, Jeremy Johnson, Shannon R. Ehmsen, Peter Kerpedjiev, Nezar Abdennur, Maxim Imakaev, Serkan Utku Öztürk, Uğur Çamoğlu, Leonid A. Mirny, Nils Gehlenborg, Burak H. Alver and Peter J. Park ()
Additional contact information
Sarah B. Reiff: Harvard Medical School
Andrew J. Schroeder: Harvard Medical School
Koray Kırlı: Harvard Medical School
Andrea Cosolo: Harvard Medical School
Clara Bakker: Harvard Medical School
Luisa Mercado: Harvard Medical School
Soohyun Lee: Harvard Medical School
Alexander D. Veit: Harvard Medical School
Alexander K. Balashov: Harvard Medical School
Carl Vitzthum: Harvard Medical School
William Ronchetti: Harvard Medical School
Kent M. Pitman: Harvard Medical School
Jeremy Johnson: Harvard Medical School
Shannon R. Ehmsen: Harvard Medical School
Peter Kerpedjiev: Harvard Medical School
Nezar Abdennur: Massachusetts Institute of Technology
Maxim Imakaev: Massachusetts Institute of Technology
Serkan Utku Öztürk: Karya SMD Software Solutions
Uğur Çamoğlu: Karya SMD Software Solutions
Leonid A. Mirny: Massachusetts Institute of Technology
Nils Gehlenborg: Harvard Medical School
Burak H. Alver: Harvard Medical School
Peter J. Park: Harvard Medical School

Nature Communications, 2022, vol. 13, issue 1, 1-11

Abstract: Abstract The 4D Nucleome (4DN) Network aims to elucidate the complex structure and organization of chromosomes in the nucleus and the impact of their disruption in disease biology. We present the 4DN Data Portal ( https://data.4dnucleome.org/ ), a repository for datasets generated in the 4DN network and relevant external datasets. Datasets were generated with a wide range of experiments, including chromosome conformation capture assays such as Hi-C and other innovative sequencing and microscopy-based assays probing chromosome architecture. All together, the 4DN data portal hosts more than 1800 experiment sets and 36000 files. Results of sequencing-based assays from different laboratories are uniformly processed and quality-controlled. The portal interface allows easy browsing, filtering, and bulk downloads, and the integrated HiGlass genome browser allows interactive visualization and comparison of multiple datasets. The 4DN data portal represents a primary resource for chromosome contact and other nuclear architecture data for the scientific community.

Date: 2022
References: View references in EconPapers View complete reference list from CitEc
Citations: View citations in EconPapers (5)

Downloads: (external link)
https://www.nature.com/articles/s41467-022-29697-4 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-29697-4

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-022-29697-4

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().