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 improvments


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 2018: a resource for experimentally validated microRNA-target interactions.

Chou CH, Shrestha S, Yang CD, Chang NW, Lin YL, Liao KW, Huang WC, Sun TH, Tu SJ, Lee WH, Chiew MY, Tai CS, Wei TY, Tsai TR, Huang HT, Wang CY, Wu HY, Ho SY, Chen PR, Chuang CH, Hsieh PJ, Wu YS, Chen WL, Li MJ, Wu YC, Huang XY, Ng FL, Buddhakosai W, Huang PC, Lan KC, Huang CY, Weng SL, Cheng YN, Liang C, Hsu WL, Huang HD*. (2018) Nucleic Acids Research. [PUBMED]

Subscription


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Current curation

Release 7.0: Sept. 15, 2017

Number of articles: 8,510

Number of species: 23

Number of target genes: 23,054

Number of miRNAs: 4,076

Number of miRNA-target interactions: 422,517


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

MethHC - A database of DNA Methylation and gene/miRNA expression in Human Cancer

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