miRBase: integrating microRNA annotation and deep-sequencing data

By Ana Kozomara, Sam Griffiths-Jones. Nucleic Acids Res., 2010

3,764 citations recorded by the source corpus.

miRBase is the primary online repository for all microRNA sequences and annotation. The current release (miRBase 16) contains over 15 000 microRNA gene loci in over 140 species, and over 17 000 distinct mature microRNA sequences. Deep-sequencing technologies have delivered a sharp rise in the rate of novel microRNA discovery. We have mapped reads from short RNA deep-sequencing experiments to microRNAs in miRBase and developed web interfaces to view these mappings. The user can view all read data associated with a given microRNA annotation, filter reads by experiment and count, and search for microRNAs by tissue- and stage-specific expression. These data can be used as a proxy for relative expression levels of microRNA sequences, provide detailed evidence for microRNA annotations and alternative isoforms of mature microRNAs, and allow us to revisit previous annotations. miRBase is available online at: http://www.mirbase.org/.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/8f7714e42d546d89d092e467532bcc66ebc90eea

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Cancer Research

In Molecular Biology

Citations in the corpus

Predicting miRNA‐disease association based on inductive matrix completion (2018, background): “(1993), since then, thousands of currently annotated miRNAs have been discovered in variety of species from plants, animals to viruses (Jopling et al., 2005; Kozomara and Griffiths-Jones, 2011).”
miRNet - dissecting miRNA-target interactions and functional associations through network-based visual analysis (2016, background): “All miRNA entries are annotated according to the latest miRBase (release 21) (25).”
miR-122--a key factor and therapeutic target in liver disease. (2015, background): “miRNAs have been identified in 206 organisms, ranging from microbes to animal species, including humans, where 2000 miRNAs are currently reported by the official miRNA repository miRBase (release 20, [3]).”
NONCODE v3.0: integrative annotation of long noncoding RNAs (2011, neutral): “0 (22), RefSeq (23), UCSC (24) and Ensembl (25).”
psRNATarget: a plant small RNA target analysis server (2017 release) (2018, background): “The psRNATarget homepage includes three functional tabs that allow users to upload and search their miRNAs against the preloaded target transcript libraries, to upload and search candidate target transcripts against published miRNA sequences downloaded from the miRBase (17), or to upload both miRNA ”
Rfam 11.0: 10 years of RNA families (2012, methodology): “Since our Wikipedia annotation project started in 2007, we have linked to 923 pages of Wikipedia content, and the Rfam-Wikipedia model has been adopted by other biological databases, such as Pfam and miRBase (9,15).”
An optimized microRNA backbone for effective single-copy RNAi. (2013, methodology): “Analysis of Sequence Motif Conservation and microRNA Representation Human pre-miRNA and mature miRNA data were obtained from miRbase (Kozomara and Griffiths-Jones, 2011), release 20.”
CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data (2013, methodology): “…user can analyze his/her own experimental data and directly compare and enrich it with publicly available information from STRING (Szklarczyk et al ., 2011), IntAct (Kerrien et al ., 2012), MiMI (Tarcea et al ., 2009), miRBase (Kozomara and Griffiths-Jones, 2011) and miRecords (Xiao et al ., 2009).”
A Guide for Functional Analysis of BRCA1 Variants of Uncertain Significance (VUS) (2012, neutral): “org/ [Kozomara and Griffiths-Jones, 2011]”
Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq (2013, positive): “(B) STARR-‐seq (cDNA) fragments from S2 cells are not substantially depleted by transcript-‐destabilizing elements: even at genomic sites that contain annotated microRNA hairpins, 3’ UTRs, splice acceptors,”
microRNAs in cancer (2013, background): “Since then, miRNAs have been discovered in virtually all plant and animal species, and the latest version of the miRNA database (miRBase), released in August 2012, catalogs 2,042 mature miRNAs in humans and 1,281 in mice (6).”