miRBase: microRNA sequences, targets and gene nomenclature

By Sam Griffiths-Jones, R. Grocock, Stijn van Dongen, Alex Bateman, Anton J. Enright. Nucleic Acids Res., 2005

4,888 citations recorded by the source corpus.

The miRBase database aims to provide integrated interfaces to comprehensive microRNA sequence data, annotation and predicted gene targets. miRBase takes over functionality from the microRNA Registry and fulfils three main roles: the miRBase Registry acts as an independent arbiter of microRNA gene nomenclature, assigning names prior to publication of novel miRNA sequences. miRBase Sequences is the primary online repository for miRNA sequence data and annotation. miRBase Targets is a comprehensive new database of predicted miRNA target genes. miRBase is available at .

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d2b4151811ed9f18013123d417c9732f93b73c49

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Citations in the corpus

microRNA-155 Regulates the Generation of Immunoglobulin Class-Switched Plasma Cells (2007, neutral): “As a control, we searched the up-regulated gene set for seed matches for all mouse miRNAs present in miRBase 9.1 (Giraldez et al., 2006; Griffiths-Jones et al., 2006).”
miRBase: tools for microRNA genomics (2007, methodology): “The target prediction pipeline and algorithms have been described elsewhere (6,7).”
Widespread deregulation of microRNA expression in human prostate cancer (2008, background): “Since these miRNAs have very similar sequences (Griffiths-Jones et al., 2006) and may potentially target similar mRNAs, such coordinate regulation may be biologically significant.”
A MicroRNA Signature of Hypoxia (2006, methodology): “For a given microRNA, these utilize different algorithms and ranking criteria (8, 18, 19) and are known to produce a partially overlapping set of candidates, making the search for targets a complex endeavor.”
The Ensembl gene annotation system (2016, methodology): “MicroRNAs (miRNAs) are annotated by an initial BLASTN search of genomic sequence against miRBase (85) stem-loop sequences, followed by filtering of the results according to E-value.”
Non-coding RNAs in Development and Disease: Background, Mechanisms, and Therapeutic Approaches. (2016, background): “Targetscan (160), miRanda(129), PicTar (143), or MicroCosm targets (89) are just some of numerous platforms available.”
microRNAs as oncogenes and tumor suppressors. (2007, background): “However, only a few of them have been experimentally validated (Griffiths-Jones et al., 2006).”
MicroRNA-34b and MicroRNA-34c are targets of p53 and cooperate in control of cell proliferation and adhesion-independent growth. (2007, background): “In contrast, Myc and Cdk6 are among predicted targets for miR-34b and E2f3, Bcl2 , and Cyclin D1 among predicted targets for miR-34c (23).”
A small piece in the cancer puzzle: microRNAs as tumor suppressors and oncogenes (2006, background): “…400 miRNAs have been identified and it is predicted that the human genome encodes up to 1000 miRNAs (Bentwich et al., 2005; Berezikov et al., 2005; Griffiths-Jones et al., 2006). miRNAs are initially transcribed by RNA polymerase II as long primary transcripts (pri-miRNAs) which are processed in…”