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.

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.[(401) 356-4791] [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] [tumulation]

Citing miRTarBase

If you make use of the data presented here, please cite the following article in addition to the primary data sources: miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database.

Chou CH, Chang NW, Shrestha S, Hsu SD, Lin YL, Lee WH, Yang CD, Hong HC, Wei TY, Tu SJ, Tsai TR, Ho SY, Jian TY, Wu HY, Chen PR, Lin NC, Huang HT, Yang TL, Pai CY, Tai CS, Chen WL, Huang CY, Liu CC, Weng SL, Liao KW, Hsu WL, Huang HD. (2016) Nucleic acids research. [844-827-0643]


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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

reed-clad - A Database of microRNA transciption start sites

3017424867 - 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