Introduction

Towards a Deep Understanding of the Genome
With advances in genome sequencing and editing technologies, our understanding of genomic information has greatly progressed. While much research has focused on the informational aspects of DNA, such as replication and epigenetic regulation, the physical properties of DNA—like stiffness, torsion, and supercoiling—remain less explored, despite their central role in genome structure and function.

Genome Modality Suite (GMS) — An Integrated Platform for Multimodal Genome Analysis

Genome Modality Suite (GMS) is a comprehensive platform designed to integrate and visualize multiple layers of genome information, focusing on both the physical properties and functional features of the genome. It consolidates diverse genomic modalities such as DNA sequence, epigenetic modifications, chromatin structure, and 3D genome architecture into a unified, intuitive interface.


[Figure 1. Schematic overview of the GM Suite]

As illustrated in Fig.1, GMS connects various data sources and provides an integrated genome coordinate-based view. Key features include:

  •  Simultaneous visualization of multiple genome data types (e.g., sequence, DNA methylation, histone modifications, Hi-C contact maps)
  •  Flexible region selection and zooming capabilities for detailed analysis
  •  Visualization of physical DNA properties such as stiffness and torsion
  •  Integration with various analytical tools to support comprehensive genome data exploration
  •  User-controlled data sharing settings, allowing users to manage their data’s visibility by choosing to make it public, private, or shared with a limited group
  •  Provision of diverse analysis tools to facilitate deeper exploration and interpretation of genome data

This platform supports genome researchers in gaining deeper insights into the relationships between genetic information, its three-dimensional organization, and physical characteristics, facilitating novel biological discoveries.

What You Can Do with GM Suite

  • Upload your own data and manage its visibility (public, private, or shared)
  • Compare your data with collaborative datasets from partner groups
  • Utilize integrated tools for structural and functional genome analysis
  • Browse curated datasets from consortium projects

  • Contribute to the research community by sharing your own genomic data

  • [Video 1. GM Suite Flyer (ver.2022)]

Getting an Account on GM Suite

To access the full features of GM Suite, you need to create a user account.


[Figure 2. Registration Page]

There are two ways to begin your registration:
Option 1: From the Login Page

  1. Go to the GM Suite portal: https://gmsuite.hgc.jp
  2. Click "Login" at the top-right corner.
  3. On the drop-down menu, click "Regist" to open the registration form.
Option 2: Direct Link

You can also directly access the registration form here:
https://gmsuite.hgc.jp/register/regist1.php

Registration Process (refer to Video 1)

  1. Enter your email address (this will serve as your account ID) and submit the form.
  2. You will receive an email titled "[GMS] Account Request", which contains an activation link.
  3. Click the activation link within 12 hours to verify your request. If the link expires, please register again.
  4. After clicking the link, you will receive another email with your login information, including:
    • Your account ID (email)
    • A temporary password
    • Login instructions

Creating a new record


[Figure 3. Dashboard & Edit pages]

After Logging into GM Suite

  • After logging into GM Suite, the user will see the "Dashboard" page (Figure 3A)
  • To create a new GMS record, click "New Submission", which will open the Edit page
  • Fill in the required fields such as Title, Experiment Type, Organism, Cell type, and others (Figure 3B)
  • Note: Keywords are extremely important. They enable links between related records and enhance data discoverability

Uploading Files

  • Click "Browse" or drag and drop files into the upload area (Figure 3C)
  • To upload all files at once, click "Upload All"
  • To upload files individually, click "Upload" next to each file
  • Confirm the acceptable file formats before uploading

Set Sharing Mode

  • Toggle the "Mode" switch to select either Public or Private (Figure 3D)
  • If set to Private and the requirements are met, you can specify other user accounts to enable limited sharing access

Showcase 1:
Reconstructing the Nanog Locus in 3D Space

The Nanog gene, a key pluripotency factor in embryonic stem cells, plays a central role in maintaining self-renewal and enabling cellular reprogramming. Its regulation is shaped not only by linear genomic sequences but also by long-range enhancer–promoter interactions and transcription factor (TF) complexes, all orchestrated within the framework of three-dimensional (3D) chromatin architecture.

In this showcase, we demonstrate how users can browse, visualize, and explore the 3D reconstruction of the Nanog locus using the GMSuite browser tools. This interactive experience allows researchers to investigate spatial gene regulation and chromatin context with integrated genomic and epigenomic layers.

    • [Showcase 1. Browsing Nonog-related GMS data]

    Bug Reporting

    We always appreciate bug reports and feedback. When you report a bug, please include the following information;

    • Reporter: Your name and email address
    • Date and time: When you saw the bug
    • URL: The page URL on which the bug occurred
    • Screen images: Attaching screen capture images
    • Expected and actual results: What our system did contradicting in expectation