miRBase: tools for microRNA genomics

By Sam Griffiths-Jones, Harpreet Kaur Saini, Stijn van Dongen, Anton J. Enright. Nucleic Acids Res., 2007

4,605 citations recorded by the source corpus.

miRBase is the central online repository for microRNA (miRNA) nomenclature, sequence data, annotation and target prediction. The current release (10.0) contains 5071 miRNA loci from 58 species, expressing 5922 distinct mature miRNA sequences: a growth of over 2000 sequences in the past 2 years. miRBase provides a range of data to facilitate studies of miRNA genomics: all miRNAs are mapped to their genomic coordinates. Clusters of miRNA sequences in the genome are highlighted, and can be defined and retrieved with any inter-miRNA distance. The overlap of miRNA sequences with annotated transcripts, both protein- and non-coding, are described. Finally, graphical views of the locations of a wide range of genomic features in model organisms allow for the first time the prediction of the likely boundaries of many miRNA primary transcripts. miRBase is available at http://microrna.sanger.ac.uk/.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2b2294ae88646efc62eb58d3383b749216f4adc3

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Citations in the corpus

Genome-wide computational identification and manual annotation of human long noncoding RNA genes. (2010, background): “To date, several hundred human microRNAs have been identified (Griffiths-Jones et al. 2008).”
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An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs (2013, background): “miRNA target miRBase [28] miRanda [20] 21,643 miRNA sequences”
Identifying miRNAs, targets and functions (2012, methodology): “EIMMo [52], miRanda [33], miRBase [53], PicTar [49], PITA [39], RNA22 [54] and TargetScan 5.”
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miRTarBase: a database curates experimentally validated microRNA–target interactions (2010, background): “miRBase (2) is the most complete repository for miRNA annotation and nomenclature.”
MicroRNAs and complex diseases: from experimental results to computational models (2019, positive): “Many miRNAs were discovered in plants, green algae, viruses and animals [36].”
Non‐coding RNAs: regulators of disease (2010, background): “In humans there are at least 700 miRNAs, hundreds of siRNAs and millions of unique piRNA sequences [15–17,45], suggesting that small RNAs are a substantial portion of the RNA output of cells and that they comprise a diverse, widespread and basal regulatory system.”
miR2Disease: a manually curated database for microRNA deregulation in human disease (2008, background): “miRBase (9), miRGator (10) and miRGen (11) aim at providing”
Biogenesis, Turnover, and Mode of Action of Plant MicroRNAs[OPEN] (2013, background): “Most MIR genes possess their own transcriptional unit (Griffiths-Jones et al., 2008); polycistronic pri-miRNA transcripts with multiple miRNA-generating hairpins have been detected but are rare in plants (Merchan et al.”
Circulating microRNAs as stable blood-based markers for cancer detection (2008, background): “miR-141 is a member of an evolutionarily conserved family of miRNAs that includes, in humans, miR-141, miR-200a, miR-200b, miR-200c, and miR-429 (19).”
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GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information (2009, background): “For example, miRBase (12) that contains putative targets of microRNAs, molecules that in the last few years have been shown as key regulators in many biological systems.”
MicroRNA-208a is a regulator of cardiac hypertrophy and conduction in mice. (2009, background): “Interestingly, the 3′ UTR of Gata4 mRNA contained a predicted miR-208a target site (Supplemental Figure 8), and so we reasoned that the miR-208a gain- and loss-of-function phenotypes might partially result from irregular GATA4 protein expression (55).”