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

Author

Listed:
  • 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
    Massachusetts Institute of Technology)

  • Nils Gehlenborg

    (Harvard Medical School)

  • Burak H. Alver

    (Harvard Medical School)

  • Peter J. Park

    (Harvard Medical School)

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.

Suggested Citation

  • 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, 2022. "The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-29697-4
    DOI: 10.1038/s41467-022-29697-4
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    Cited by:

    1. Jacques Serizay & Cyril Matthey-Doret & Amaury Bignaud & Lyam Baudry & Romain Koszul, 2024. "Orchestrating chromosome conformation capture analysis with Bioconductor," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    2. Thais Ealo & Victor Sanchez-Gaya & Patricia Respuela & María Muñoz-San Martín & Elva Martin-Batista & Endika Haro & Alvaro Rada-Iglesias, 2024. "Cooperative insulation of regulatory domains by CTCF-dependent physical insulation and promoter competition," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
    3. Dan Daniel Erdmann-Pham & Sanjit Singh Batra & Timothy K. Turkalo & James Durbin & Marco Blanchette & Iwei Yeh & Hunter Shain & Boris C. Bastian & Yun S. Song & Daniel S. Rokhsar & Dirk Hockemeyer, 2023. "Tracing cancer evolution and heterogeneity using Hi-C," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    4. Tengfei Wang & Shuxiang Shi & Yuanyuan Shi & Peipei Jiang & Ganlu Hu & Qinying Ye & Zhan Shi & Kexin Yu & Chenguang Wang & Guoping Fan & Suwen Zhao & Hanhui Ma & Alex C. Y. Chang & Zhi Li & Qian Bian , 2023. "Chemical-induced phase transition and global conformational reorganization of chromatin," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    5. Shuzhen Kuang & Katherine S. Pollard, 2024. "Exploring the roles of RNAs in chromatin architecture using deep learning," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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