PiRTarBase: A database of piRNA targeting sites and their roles in gene regulation

Wei-Sheng Wu, Jordan S. Brown, Tsung Te Chen, Yu Han Chu, Wei Che Huang, Shikui Tu, Heng Chi Lee

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

PIWI-interacting RNAs (piRNAs) are a class of small noncoding RNAs that guard animal genomes against mutation by silencing transposons. In addition, recent studies have reported that piRNAs silence various endogenous genes. Tens of thousands of distinct piRNAs made in animals do not pair well to transposons and currently the functions and targets of piRNAs are largely unexplored. piRTarBase provides a user-friendly interface to access both predicted and experimentally identified piRNA targeting sites in Caenorhabditis elegans. The user can input genes of interest and retrieve a list of piRNA targeting sites on the input genes. Alternatively, the user can input a piRNA and retrieve a list of its mRNA targets. Additionally, piRTarBase integrates published mRNA and small RNA sequencing data, which will help users identify biologically relevant targeting events. Importantly, our analyses suggest that the piRNA sites found by both predictive and experimental approaches are more likely to exhibit silencing effects on their targets than each method alone. Taken together, piRTarBase offers an integrative platform that will help users to identify functional piRNA target sites by evaluating various information. piRTarBase is freely available for academic use at http://cosbi6.ee.ncku.edu.tw/piRTarBase/.

Original languageEnglish
Pages (from-to)D181-D187
JournalNucleic acids research
Volume47
Issue numberD1
DOIs
Publication statusPublished - 2019 Jan 8

Fingerprint

Small Interfering RNA
Databases
RNA
Genes
RNA Sequence Analysis
Small Untranslated RNA
Messenger RNA
Caenorhabditis elegans
Genome
Mutation

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Wu, W-S., Brown, J. S., Chen, T. T., Chu, Y. H., Huang, W. C., Tu, S., & Lee, H. C. (2019). PiRTarBase: A database of piRNA targeting sites and their roles in gene regulation. Nucleic acids research, 47(D1), D181-D187. https://doi.org/10.1093/nar/gky956
Wu, Wei-Sheng ; Brown, Jordan S. ; Chen, Tsung Te ; Chu, Yu Han ; Huang, Wei Che ; Tu, Shikui ; Lee, Heng Chi. / PiRTarBase : A database of piRNA targeting sites and their roles in gene regulation. In: Nucleic acids research. 2019 ; Vol. 47, No. D1. pp. D181-D187.
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Wu, W-S, Brown, JS, Chen, TT, Chu, YH, Huang, WC, Tu, S & Lee, HC 2019, 'PiRTarBase: A database of piRNA targeting sites and their roles in gene regulation', Nucleic acids research, vol. 47, no. D1, pp. D181-D187. https://doi.org/10.1093/nar/gky956

PiRTarBase : A database of piRNA targeting sites and their roles in gene regulation. / Wu, Wei-Sheng; Brown, Jordan S.; Chen, Tsung Te; Chu, Yu Han; Huang, Wei Che; Tu, Shikui; Lee, Heng Chi.

In: Nucleic acids research, Vol. 47, No. D1, 08.01.2019, p. D181-D187.

Research output: Contribution to journalArticle

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