MNDR v3.0: mammal ncRNA–disease repository with increased coverage and annotation

Abstract

Many studies have indicated that non-coding RNA (ncRNA) dysfunction is closely related to numerous diseases. Recently, accumulated ncRNA–disease associations have made related databases insufficient to meet the demands of biomedical research. The constant updating of ncRNA–disease resources has become essential. Here, we have updated the mammal ncRNA–disease repository (MNDR, http://www.rna-society.org/mndr/) to version 3.0, containing more than one million entries, four-fold increment in data compared to the previous version. Experimental and predicted circRNA–disease associations have been integrated, increasing the number of categories of ncRNAs to five, and the number of mammalian species to 11. Moreover, ncRNA–disease related drug annotations and associations, as well as ncRNA subcellular localizations and interactions, were added. In addition, three ncRNA–disease (miRNA/lncRNA/circRNA) prediction tools were provided, and the website was also optimized, making it more practical and user-friendly. In summary, MNDR v3.0 will be a valuable resource for the investigation of disease mechanisms and clinical treatment strategies.

Identifying potential biomarkers in hepatitis B virus infection and its response to the antiviral therapy by integrated bioinformatic analysis

“…The MNDR online platform ( http://www.rna‐society.org/mndr/home.html ) was designed for efficient browsing the associations between ncRNA (including lncRNA, miRNA, piRNA, snoRNA) and diseases in mammals. 15 By browsing the mesh terms or the disease ontology ‘hepatitis B/hepatitis B, chronic’, the disease‐related ncRNAs were downloaded from MNDR v3.1. In this study, we restricted the ‘species’ to ‘Homo sapiens’ and only included ncRNA‐disease associations that were evaluated as ‘Strong Evidence’ by MNDR v3.1 platform.…”

BiGAN: LncRNA-disease association prediction based on bidirectional generative adversarial network

“…The first dataset is from the mammalian ncRNA disease repository (MNDR) with coverage and annotation proposed by Lin et al 24 August 2020 [ 39 ]. We extracted association information about human lncRNA-disease pairs in MNDR, consisting of two datasets.…”

GeneCodis 4: Expanding the modular enrichment analysis to regulatory elements

“…The regulatory category contains two curated interactomes TF-gene pairs from DoRothEA and miRNA-gene interactions derived from strong evidence techniques such as: reporter assay, western blot and qRT-PCR from miRTarBase (Huang et al, 2020). Moreover, as a specialised regulatory subcategory, miRNAs-based functional annotations are added from the Tool for miRNA Set Analysis (TAM) database (Li et al, 2018), the Human microRNA Disease Database (HMDD) (Huang et al, 2019) and the Mammalian ncRNA-Disease Repository (MNDR) (Ning et al, 2021). miRNAs-based annotations mainly contain miRNAs-disease associations, only TAM includes functional categories but compared to gene-based databases it still lacks a comprehensive annotation, however it should be considered as the first option to overcome the miRNA enrichment analysis.…”