MirGeneDB

MirGeneDB curates and catalogs manually validated microRNA genes across metazoan species using uniform annotation criteria and phylogenetically informed nomenclature.

Key Features:

• Manual curation: All microRNA entries are manually curated to exclude false positives and false negatives based on mechanistically understood features that distinguish bona fide miRNAs from other small RNAs.
• Phylogenetically informed nomenclature: The database employs a consistent naming system based on evolutionary hierarchy and refined evolutionary nodes of origin for microRNA families and genes.
• Taxonomic expansion: MirGeneDB 3.0 contains 21,822 microRNA genes from 1,743 families across 114 metazoan species, including representatives of previously unsampled phyla such as sponges, jellyfish, rotifers, and flatworms.
• Expression data availability: SmallRNA read data and microRNA expression matrices for all tissues and species are downloadable.
• Covariance models: Updated covariance models of all microRNA families are provided for download to enable analysis of secondary structure and biogenesis features.
• Version tracking: A specifically developed version tracker records all changes to annotations and nomenclature.
• Novel microRNA naming authority: MirGeneDB 3.0 assumes responsibility for naming conserved novel metazoan microRNAs.
• Integration: The database is part of RNAcentral and Elixir Norway.

Scientific Applications:

• Comparative microRNA genomics: The curated complements enable reconstruction of ancestral miRNA repertoires and study of microRNA innovation across approximately 800 million years of animal evolution.
• Whole genome duplication studies: Inclusion of phylogenetically important species relevant for studying whole genome duplication events refines understanding of microRNA family evolution.
• Biomarker and biomedical research: The robust platform supports deeper insights into microRNA biology applicable to human disorders and biomarker discovery.
• microRNA property analysis: Researchers can analyze secondary structure and biogenesis features within a robust phylogenetic context.
• Sequence evolution studies: The database distinguishes mature versus star products to enable analysis of their different tempos and modes of sequence evolution.

Methodology:

MicroRNA genes are annotated using uniform and consistent criteria based on mechanistically well understood features that distinguish bona fide miRNAs from other small RNAs; entries are manually curated and named according to a phylogenetically informed nomenclature system with traceable version tracking.