miRTarBase: a database curates experimentally validated microRNA–target interactions

By Sheng-Da Hsu, F. Lin, Wei-Yun Wu, Chao Liang, Wei-Chih Huang, Wen-Ling Chan, Wen-Ting Tsai, Goun-Zhou Chen, Chia-Jung Lee, Chih-Min Chiu and 5 more. Nucleic Acids Res., 2010

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MicroRNAs (miRNAs), i.e. small non-coding RNA molecules (∼22 nt), can bind to one or more target sites on a gene transcript to negatively regulate protein expression, subsequently controlling many cellular mechanisms. A current and curated collection of miRNA–target interactions (MTIs) with experimental support is essential to thoroughly elucidating miRNA functions under different conditions and in different species. As a database, miRTarBase has accumulated more than 3500 MTIs by manually surveying pertinent literature after data mining of the text systematically to filter research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assays, western blot, or microarray experiments with overexpression or knockdown of miRNAs. miRTarBase curates 3576 experimentally verified MTIs between 657 miRNAs and 2297 target genes among 17 species. miRTarBase contains the largest amount of validated MTIs by comparing with other similar, previously developed databases. The MTIs collected in the miRTarBase can also provide a large amount of positive samples to develop computational methods capable of identifying miRNA–target interactions. miRTarBase is now available on http://miRTarBase.mbc.nctu.edu.tw/, and is updated frequently by continuously surveying research articles.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7bdafc53f96f0282c17b082a41b67d76cb24d957

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Citations in the corpus

RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse (2015, background): “For post-transcriptional regulations, the experimentally validated ‘miRNA–gene’ pairs in human and mouse from miRTarBase (33), TarBase (37) and miRecords (32) are directly deposited in RegNetwork.”
PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways (2013, background): “We have collected >14 000 new experimentally supported miRNA–mRNA interactions from two recently updated databases, miRecords (35) and miRTarBase (36).”
TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support (2011, background): “miRTarBase (14) was first released in 2010.”
NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis (2019, methodology): “TarBase (19) and miRTarbase (20) have been used to obtain experimentally validated miRNA–gene target information, while ENCODE (21), JASPAR (22) and CHEA (23) have been used to obtain TF–gene target Users can double click a meta-node (large semi-transparent circles) to view all its associated genes…”
The multiMiR R package and database: integration of microRNA–target interactions along with their disease and drug associations (2014, background): “The multiMiR database contains human and mouse data from 14 external databases that are categorized into three components (Figure 1), including the three validated miRNA–target databases (miRecords (27), miRTarBase (28) and TarBase (26)), the eight predicted miRNA– target databases (DIANA-microT (12”
Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding (2013, neutral): “Cognate miRNA-mRNA pairs identified by CLASH and represented in the miRNA depletion data set were retrospectively analyzed and compared to confirmed miRNA-mRNA pairs from miRTarBase (Hsu et al., 2011).”
Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers (2015, methodology): “In particular, we have referred to previous studies and selected lncRNA-cancer associations for manual curation using strict criteria (31).”
miRWalk - Database: Prediction of possible miRNA binding sites by "walking" the genes of three genomes (2011, background): “1) [43] databases on which miRNA binding sites are already verified and published in the PubMed database.”
miRNet - dissecting miRNA-target interactions and functional associations through network-based visual analysis (2016, methodology): “The miRNAtarget interaction data were downloaded from 11 wellannotated databases including miRTarBase (13), TarBase D ow naded rom http/academ ic.”
starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data (2013, result): “These results coincide with data in an experimentally validated database named miRTarBase (40), suggesting that these genes are likely targeted by hsa-miR-21-5p.”