miRBase: from microRNA sequences to function

By Ana Kozomara, Maria Birgaoanu, Sam Griffiths-Jones. Nucleic Acids Res., 2018

3,854 citations recorded by the source corpus.

Abstract miRBase catalogs, names and distributes microRNA gene sequences. The latest release of miRBase (v22) contains microRNA sequences from 271 organisms: 38 589 hairpin precursors and 48 860 mature microRNAs. We describe improvements to the database and website to provide more information about the quality of microRNA gene annotations, and the cellular functions of their products. We have collected 1493 small RNA deep sequencing datasets and mapped a total of 5.5 billion reads to microRNA sequences. The read mapping patterns provide strong support for the validity of between 20% and 65% of microRNA annotations in different well-studied animal genomes, and evidence for the removal of >200 sequences from the database. To improve the availability of microRNA functional information, we are disseminating Gene Ontology terms annotated against miRBase sequences. We have also used a text-mining approach to search for microRNA gene names in the full-text of open access articles. Over 500 000 sentences from 18 542 papers contain microRNA names. We score these sentences for functional information and link them with 12 519 microRNA entries. The sentences themselves, and word clouds built from them, provide effective summaries of the functional information about specific microRNAs. miRBase is publicly and freely available at http://mirbase.org/.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/84a22808313c4452b0e0611c3c9d3ab7b37a2cab

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Citations in the corpus

miRTarBase update 2022: an informative resource for experimentally validated miRNA–target interactions (2021, background): “Currently, >35 000 miRNA sequences have been identified in >270 organisms (2).”
Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development (2021, methodology): “We use miRBase (Kozomara et al. 2019) to obtain miRNA mature sequence as the feature representation for miRNAs.”
Exploration of prognosis-related microRNA and transcription factor co-regulatory networks across cancer types (2019, methodology): “We unified TF/miRNA/ target gene symbols in the regulatory relationship by referring the Hugo Gene Nomenclature Committee (HGNC) [66], the approval TF list [67,68], and miRBase [69].”
miRDB: an online database for prediction of functional microRNA targets (2019, background): “About 2000 human miRNAs have been reported in miRBase (3).”
Rfam 14: expanded coverage of metagenomic, viral and microRNA families (2020, background): “MicroRNA sequences and annotations are aggregated in miRBase (40), the authoritative resource for published microRNA genes.”
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases (2020, methodology): “The search has been integrated into Rfam (6), miRBase (17) and snoDB (18).”
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.”
Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis (2020, neutral): “As the Reviewer suggested, we have restructured the manuscript.”
Genenames.org: the HGNC and VGNC resources in 2021 (2020, methodology): “Since September 2018, we have also named 60 microRNAs in collaboration with miRBase (27), 15 transfer RNAs in collaboration with GtRNAdb (28), and 8 variant small nuclear RNAs following consultation with our specialist advisor Dawn O’Reilly.”