Genome Modality Suite

Accelerating progress toward
the understanding of multi-scale genome properties

 DB Status: OK

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  • (Examples: Mesoscale, Stiffness, NANOG, Sperm, HeLa)

    • Explore the full spectrum of GMSuite data 

    Learn how to use GMSuite 

    Database

    Accessing and exploring GMS data

    Genome Browser

    Browsing multi-modal genome data

    Protein Viewer

    Interactive visualizing multiple 3D proteins

    Single-cell Browser

    Interactive single-cell data browsing

    1.17

    TB files

    Records

    Tissues/Cells

    Users

    Multi-scale Genome Modality

    Nanoscale
    Perspectives on DNA structure at the molecular level
    (e.g., Stiffness)
    Mesoscale
    Modeling spatial structures such as chromatin fibers and chromosomes
    (e.g., Condensation)
    Nuclear-scale
    Exploring 2D&3D chromatin formation within the entire nucleus
    (e.g., Contacts)
    Genome DNA
    Comprehensive genome sequences and structural features of organisms
    Spotlight
    GMS-65-6: Condensed but liquid-like domain organization of active chromatin regions in liv...
    Synthetic DNA
    Functional analysis and applications using artificially synthesized DNA
    Cell Cycle
    Changes in genome architecture across different cell cycle phases
    Development
    Understanding genome properties during developmental processes
    Disease
    Multi-scale genomic/epigenomic abnormalities related to diseases

     Tools

    Latest Records
    GMS-65-113 (2025-06-04 17:46:22)
    Intra-chromosomal Hi-C contacts in mESC 3.47 GB

    GMS-58-7 (2025-06-03 10:32:17)

    GMS-176-2 (2025-06-02 17:40:53)

    GMS-176-1 (2025-06-02 16:58:48)

    GMS-64-3 (2025-05-21 22:33:26)
    Introduction of GM Suite (Ver 0.5) 114.73 MB

    [more...]


    What's New
    •  Xenopus laevis (xenLae10) is now browsable (2025/05/28)
    •  SpaceWalk with a PHi-C2 model is now available GMS-65-113_765 (2025/05/20)
    •   PHi-C2 "Stiffness" & "Liquid-like" prediction is now available GMS-65-113_765 (2025/05/14)
    •   Cell-type annotation by ceLLama is now available. GMS-64-84 (2025/05/2)
    •   Single-cell Cell Browser is now available.  (2025/04/20)
    •   Transcriptome during mouse germ-cell development is available. GMS-64-82 and GMS-64-83 (2025/03/31)
      Searchable for genes related to PGC & Spermatogenesis
    •   PDB and mmCIF are uploadable. GMS-64-1 (2025/03/24)
    •   Motif enrichment analysis within boundaries and anchors is now available (2024/12/14)
    •   4DN domain calling is now available (2024/11/14)
    •   deepTools (ver. 3.5.4) has been installed (2024/11/01)
    •   HicExplorer (ver. 3.7.5) has been installed (2024/10/25)
    •   Domain calling with hic data is now available
       ArrowHead, Diamond-insulation,
       hicDetectLoops, HicCups&APA …
       (2023/12/29)
    •   set --accept .mcool
       (automatically converted into .hic) …
       (2023/12/23)
    •   set --accept .bedGraph.gz … (2023/11/10)
    •   set --install EPI (ABC model)… (2023/02/02)
    •   set --update JBrowse2 … (2023/01/12)
    •   set --create Introduction Movie… (2023/01/10)
    •   set --update PHi-C2 … (2022/04/10)
    •   set --install JuiceBox … (2022/02/18)
    •   set --install JBrowse2 … (2021/11/12)
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