Surreal illustration of microRNA-disease interactions.

Decoding microRNAs: How HMDD v3.0 Is Revolutionizing Disease Research

Kai Mendoza in Science & Nature September 2025 • 4 min read.

"Unlocking the Secrets of miRNA-Disease Associations for Better Diagnostics and Therapies"

In the ever-evolving world of biomedical research, understanding the intricate connections between microRNAs (miRNAs) and human diseases is crucial. miRNAs, small non-coding RNA molecules, play a pivotal role in regulating gene expression, influencing a wide array of biological processes. When these miRNAs go awry, they can contribute to the development and progression of various diseases, including cancer, cardiovascular disorders, and neurodegenerative conditions.

To unravel these complex relationships, scientists rely on comprehensive databases that meticulously catalog miRNA-disease associations. One such database that has emerged as a game-changer in the field is the Human MicroRNA Disease Database (HMDD). With the recent release of its third version (HMDD v3.0), this valuable resource has undergone significant enhancements, offering researchers a wealth of experimentally-supported data and advanced functionalities.

HMDD v3.0 stands as a testament to the power of data-driven discovery. By manually curating a vast collection of miRNA-disease association entries from scientific literature, this database empowers researchers to explore the roles of miRNAs in disease, develop novel diagnostic tools, and design targeted therapies. The database is freely accessible, ensuring that scientists worldwide can leverage its resources to advance their understanding of human health and disease.

What Makes HMDD v3.0 a Breakthrough in miRNA Research?

Surreal illustration of microRNA-disease interactions.

HMDD v3.0 isn't just an incremental update; it's a substantial leap forward compared to its predecessor, HMDD v2.0. The new version boasts a wealth of improvements that make it an indispensable tool for miRNA researchers:

The most striking enhancement is the sheer volume of data. HMDD v3.0 contains over 32,281 experimentally supported miRNA-disease association entries, which is roughly twice the number found in HMDD v2.0. This expanded dataset provides a much more comprehensive view of the miRNA-disease landscape.

Enhanced Data Coverage: Doubling the number of entries significantly broadens the scope of research possibilities.
Accurate Classification: Associations are meticulously classified based on evidence, enhancing data reliability.
Functional Enrichment Analysis: Provides insight into the function of miRNA target genes, aiding researchers in understanding biological roles.

One of the most valuable additions to HMDD v3.0 is the refined classification system for miRNA-disease associations. The database now categorizes these associations based on literature-derived evidence codes, resulting in six generalized categories: genetics, epigenetics, target interactions, circulation, tissue expression, and other mechanisms. These categories are further divided into 20 types of detailed evidence codes, offering a granular understanding of the experimental support for each association. This detailed classification empowers researchers to assess the confidence level of each miRNA-disease association, ensuring they can focus on the most robust and reliable data.

The Future of miRNA Research with HMDD

HMDD v3.0 represents a significant leap forward in our ability to understand the complex interplay between microRNAs and human disease. By providing a comprehensive, well-organized, and easily accessible resource, HMDD v3.0 empowers researchers to accelerate their discoveries and develop innovative solutions for diagnosing, treating, and preventing a wide range of diseases. The database is poised to play a pivotal role in shaping the future of precision medicine.

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This article is based on research published under:

DOI-LINK: 10.1093/nar/gky1010, Alternate LINK

Title: Hmdd V3.0: A Database For Experimentally Supported Human Microrna–Disease Associations

Subject: Genetics

Journal: Nucleic Acids Research

Publisher: Oxford University Press (OUP)

Authors: Zhou Huang, Jiangcheng Shi, Yuanxu Gao, Chunmei Cui, Shan Zhang, Jianwei Li, Yuan Zhou, Qinghua Cui

Published: 2018-10-26

Everything You Need To Know

What is the Human MicroRNA Disease Database (HMDD v3.0) and why is it important?

The Human MicroRNA Disease Database (HMDD v3.0) is a comprehensive database that catalogs experimentally-validated data on microRNA (miRNA)-disease associations. It's crucial because miRNAs, small non-coding RNA molecules, regulate gene expression and are implicated in various diseases. HMDD v3.0 provides researchers with a wealth of data to understand these complex relationships, aiding in the development of new diagnostic and therapeutic strategies for conditions like cancer, cardiovascular disorders, and neurodegenerative diseases. It acts as a central hub for information, allowing scientists to explore the roles of miRNAs in disease.

How does HMDD v3.0 improve upon its previous version, HMDD v2.0?

HMDD v3.0 offers significant enhancements over HMDD v2.0. The most notable upgrade is the increased data volume, with over 32,281 experimentally supported miRNA-disease association entries, doubling the number found in HMDD v2.0. This expansion provides a more comprehensive view of the miRNA-disease landscape. Furthermore, HMDD v3.0 introduces a refined classification system. This system categorizes miRNA-disease associations based on literature-derived evidence codes across six generalized categories (genetics, epigenetics, etc.), further divided into 20 detailed evidence types. This granular classification allows researchers to assess the reliability of each association more effectively.

What are microRNAs (miRNAs) and how do they relate to diseases?

MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression. They play a critical role in influencing a wide range of biological processes. When miRNAs malfunction, they can contribute to the development and progression of various diseases. This disruption in regulation can lead to the dysregulation of cellular pathways, ultimately contributing to conditions like cancer, cardiovascular disorders, and neurodegenerative diseases. HMDD v3.0 is designed to help researchers understand these complex connections.

How does the classification system in HMDD v3.0 help researchers?

The classification system within HMDD v3.0 categorizes miRNA-disease associations based on evidence codes derived from scientific literature. These associations are grouped into six generalized categories and further subdivided into 20 detailed evidence types. This system allows researchers to assess the confidence level of each miRNA-disease association, enabling them to focus on the most reliable and robust data. This detailed classification facilitates a more in-depth understanding of the experimental support for each association, guiding researchers in their investigations and ensuring the validity of their findings.

How can HMDD v3.0 contribute to the future of precision medicine?

HMDD v3.0 is poised to play a pivotal role in the future of precision medicine by providing a comprehensive, well-organized, and easily accessible resource. By offering a vast collection of experimentally-validated miRNA-disease associations, it empowers researchers to accelerate their discoveries and develop innovative solutions. This resource can be used to create more targeted diagnostics, enabling earlier and more accurate disease detection. Furthermore, it can facilitate the design of personalized therapies that target specific miRNAs involved in disease development, ultimately leading to more effective treatments and preventive measures tailored to individual patients.