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Manual, Data Source, Related Databases

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  • (1) Enter the name of the miRNA or gene of interest (fuzzy search is supported). (2) Click "Search". (3) Wait for the search results.
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    Search
    FAQs
    The search function offers multiple search options.
    1. By miRNA
    Search using miRNA names based on the miRBase standard, as shown in the examples below:
    FAQs
    2. By Target Gene
    Search using gene symbols, as shown in the examples below:
    FAQs
    3. By Pathway
    Search based on KEGG Pathway, as shown in the examples below:
    FAQs
    4. By Validated Method
    Search using various methods for validating miRNA-target gene interactions, as shown in the examples below:
    FAQs
    5. By miRNA
    Search by disease, as illustrated below:
    FAQs
    6. By Literature
    Search by article PMID, as demonstrated below:
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    7. Advanced Search
    Advanced search function: supports searching multiple miRNAs or genes at once, as illustrated below:
    FAQs
    Search Result
    FAQs
    Each miRNA-target gene record is assigned a unique miRNA-target interaction ID (referred to as MIRTID), such as MIRT000012. For search results, filtering can be done based on the reliability of experimental evidence.
    Detailed Information on the Reusult
    FAQs
    Browse information related to the MTI by different categories: miRNA, target gene, evidence, expression, TCGA, gene set enrichments, miRNA-drug associations, and network.
    Browse
    FAQs
    The browse interface allows viewing all miRNAs, target genes, and diseases (along with their respective record counts, sorted from highest to lowest) as well as different species.
    Download
    Generally, when dealing with a large number of miRNAs, it is best to download the data for local analysis. miRTarBase conveniently offers a download page that contains more comprehensive data for download.
    FAQs FAQs FAQs
  • Western blot
    • After gel electrophoresis, transfer protein to membrane and then using antibody to detect protein expression.

    Reference: Pubmed  Graph Resource


  • Luciferase reporter assay
    • The method can help to detect whether the miRNA is binding to mRNA or not.

    Reference: Pubmed  Graph Resource


  • GFP reporter assay
    • Using green fluorescent protein to detect whether the mRNA is effect by miRNA and then change the protein expression.

    Reference: Pubmed  Graph Resource


  • RT-PCR
    • Reverse transcriptase-PCR, the technique using reverse transcriptase transforms mRNA into cDNA. And then using PCR to amplify to detect the mRNA expression.

    Reference: Pebmed  Graph Resource


  • pSILAC
    • Pulsed SILAC (stable-isotope labeling by amino acids in cultured cells), the method can detect protein abundance.

    Reference: Pubmed


  • Microarray
    • It is a high-throughput method to detect differentially expression mRNAs by the probe and sample hybridization.

    Reference: Pubmed  Graph Resource


  • Branched DNA probe assay
    • The assay can detect and RNA or DNA target and quantified the target sample.

    Reference: Pubmed


  • Northern blot
    • After gel electrophoresis, transform RNA onto membrane and using labeled probe to detect RNA expression.

    Reference: Pubmed
    1. Other Experimentally Verified miRNA Target Resources
  • TarBase (Papadopoulos GL et al., Nucleic Acids Res. 2009)
  • miRecords (Xiao F et al., Nucleic Acids Res. 2009)
  • miR2Disease (Jiang Q. et al, Nucleic Acids Res. 2009)
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    2. Other Predicted miRNA Target Resources
  • miRNAMap (Hsu SD et al., Nucleic Acids Res. 2008)
  • miRBase (Griffiths-Jones S et al., Nucleic Acids Res. 2008)
  • TargetScanS (Benjamin P. Lewis et al, Cell 2005)
  • microRNA.org (Betel D et al, Nucleic Acids Res. 2008)
  • miRDB (Xiaowei Wang, RNA 2008)
  • miRGator (Seungyoon Nam et al, Nucleic Acids Res. 2008)
  • miRGen (Panagiotis Alexiou et al, Nucleic Acids Res. 2009)
  • PicTar(Azra Krek et al, Nature Genetics 2005)
  • RNA22(Ang, W.-L. et al, Cell 2006)
  • DIANA MicroT (Maragkakis; P. A. et al, BMC Bioinformatics 2009)
  • MicroInspector (Ventsislav R. et al, Nucleic Acids Res. 2005)
  • miRU (Yuanji Zhang, Nucleic Acids Rds. 2005)
  • TAPIR (Bonnet E. et al, Bioinformatics 2010)
  • RNAhybrid (Krüger J. et al, Nucleic Acids Res. 2006)
  • miRo (Laganà A. et al, Database 2009)
  • miRSel (Naeem H. et al, BMC Bioinformatics 2010)
  • MirOrtho (Gerlach D. et al, Nucleic Acids Res. 2009)
  • Patrocles (Hiard S. et al, Nucleic Acids Res. 2010)
  • miRNAtools
  • miRNA – Target Gene Prediction at EMBL (Stark A et al, Cell 2005)
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    3. Databases that are integrated by miRTarBase
  • miRBase (Kozomara, Ana et al., Nucleic Acids Res. 2019)
  • NCBI Entrez gene (Maglott, Donna et al., Nucleic Acids Res. 2011)
  • NCBI RefSeq (O'Leary, Nuala A et al., Nucleic Acids Res. 2016)
  • dbSNP (Sherry, S T et al., Nucleic Acids Res. 2001)
  • GWAS Catalog (Buniello, Annalisa et al., Nucleic Acids Res. 2019)
  • ClinVar (Landrum, Melissa J et al., Nucleic Acids Res. 2020)
  • COSMIC (Tate, John G et al., Nucleic Acids Res. 2019)
  • HMDD (Huang, Zhou et al., Nucleic Acids Res. 2019)
  • TransMir (Tong, Zhan et al., Nucleic Acids Res. 2019)
  • miRSponge (Wang, Peng et al., Database. 2015)
  • TissueAtlas (Ludwig, Nicole et al., Nucleic Acids Res. 2016)
  • EVmiRNA (Liu, Teng et al., Nucleic Acids Res. 2019)
  • Gene Expression Omnibus (GEO) (Barrett, Tanya et al., Nucleic Acids Res. 2013)
  • The Cancer Genome Atlas (TCGA) (Deng, Mario et al., BMC bioinformatics. 2016)
  • CMEP (Li, Jian-Rong et al, Bioinformatics. 2019)
  • MiREDiBase (Marceca, Gioacchino P et al., Scientific data. 2021)
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