HMDD v3.0: a database for experimentally supported human microRNA–disease associations

By Zhou Huang, Jiangcheng Shi, Yuanxu Gao, Chunmei Cui, Shan Zhang, Jianwei Li, Yuan Zhou, Qinghua Cui. Nucleic Acids Res., 2018

675 citations recorded by the source corpus.

Abstract Comprehensive databases of microRNA–disease associations are continuously demanded in biomedical researches. The recently launched version 3.0 of Human MicroRNA Disease Database (HMDD v3.0) manually collects a significant number of miRNA–disease association entries from literature. Comparing to HMDD v2.0, this new version contains 2-fold more entries. Besides, the associations have been more accurately classified based on literature-derived evidence code, which results in six generalized categories (genetics, epigenetics, target, circulation, tissue and other) covering 20 types of detailed evidence code. Furthermore, we added new functionalities like network visualization on the web interface. To exemplify the utility of the database, we compared the disease spectrum width of miRNAs (DSW) and the miRNA spectrum width of human diseases (MSW) between version 3.0 and 2.0 of HMDD. HMDD is freely accessible at http://www.cuilab.cn/hmdd. With accumulating evidence of miRNA–disease associations, HMDD database will keep on growing in the future.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0f1c1621310a7f392aa3a31b302175014946fdf5

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In Cancer Research

1. Jianguo Xia
2. Le Chang
3. Guangyan Zhou
4. Othman Soufan

In Molecular Biology

1. Guangyan Zhou
2. Othman Soufan
3. Le Chang
4. Jianguo Xia
5. David S. Wishart
6. Jasmine Chong
7. Igor Sinelnikov

Citations in the corpus

• miRNet 2.0: network-based visual analytics for miRNA functional analysis and systems biology (2020, methodology): “We have updated the miRNA interaction knowledgebase based on the latest releases from major miRNA annotation databases including miRBase (24), miRTarBase (25), TarBase (26), HMDD (27) etc.”
• miRTarBase update 2022: an informative resource for experimentally validated miRNA–target interactions (2021, methodology): “In detail, miRNA regulatory information was collected from TransmiR (32) and miRSponge (33); SNPs and DRVs were collected from dbSNP (15), GWAS Catalog (16), ClinVar (17) and COSMIC (18); disease associations were obtained from HMDD (34); gene and miRNA expression profiles, including circulating and”
• miRTarBase 2020: updates to the experimentally validated microRNA–target interaction database (2019, methodology): “List of the databases that are integrated by miRTarBase Type Database name Gene and miRNA-specific databases miRBase (7), NCBI Entrez gene (29), NCBI RefSeq (30) SNP or mutation related databases SomamiR (22,31) miRNA–disease association Database HMDD (9,10) The regulation of miRNAs TransMir (19), m”
• Non-coding RNAs in disease: from mechanisms to therapeutics (2023, neutral): “Several databases, such as The Human MicroRNA Disease Database 101 for miRNAs and LncRNADisease 102,103 for lncRNAs and circRNAs, can be useful resources for up-to-date information on disease-related ncRNAs.”