miRTarBase: the experimentally validated microRNA-target interactions database

As a database, miRTarBase has accumulated more than three hundred and sixty thousand miRNA-target interactions (MTIs), which are collected by manually surveying pertinent literature after NLP of the text systematically to filter research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments. While containing the largest amount of validated MTIs, the miRTarBase provides the most updated collection by comparing with other similar, previously developed databases.

Major improvements

New Features

1. The word cloud of miRNA-disease information
  • Example: hsa-miR-122-5p shows the miRNA was major related to the liver related disease such as hepatocellular carcinoma.
2. miRNA-Target site viewer in CLIP-seq data
  • Example: The miRNA, hsa-miR-15a-5p :: VEGFA, target gene was display in 17 CLIP-seq (HITS-CLIP and PAR-CLIP) data sets generated by 6 independent studies.[17 datasets] [CLIP-seq Viewer]
3. Clinical microRNA and gene expression profiles from TCGA
  • Example: hsa-miR-122-5p is a tumor suppressor and targets ALDOA in hepatocellular carcinoma. Also, only hepatocellular carcinoma shows significant negative correlation (P-value=3.9e-7 and R=-0.639) in TCGA data. [9 cancers] [HCC]

Citing miRTarBase

If you make use of the data presented here, please cite the following article in addition to the primary data sources:miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions.

Hsu SD, Tseng YT, Shrestha S, Lin YL, Khaleel Anas, Chou CH, Chu CF, Huang HY, Lin CM, Ho SY, Jian TY, Lin FM, Chang TH, Weng SL, Liao KW, Liao IE, Liu CC and Huang HD. (2014) Nucleic acids research. [ PUBMED ]


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Current curation

Release 6.0: Sept. 15, 2015

Number of articles: 4,966

Number of species: 18

Number of target genes: 22,563

Number of miRNAs: 3,786

Number of miRNA-target interactions: 366,181

MicroRNA resources from ISBLAB

miRTar - An integrated web server for identifying miRNA-target interactions

miRTarCLIP - A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing

miRStart - A Database of microRNA transciption start sites

miRNAMap - Genomic maps of microRNAs in metazoan genomes

VITA - Prediction of host microRNAs targets on viruses

RegRNA - An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs

miRExpress - Analyzing high-throughput sequencing data for profiling microRNA expression