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RefFinder: a web-based tool for comprehensively analyzing and identifying reference genes

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Abstract

Although many genes may serve as reference genes, they may cause different expression patterns by selecting different reference genes because no single gene is expressed consistently in all tested tissues of an organism under all environmental and developmental conditions. Thus, it is becoming increasingly important and necessary to identify suitable reference genes before performing gene expression analysis. Currently, there are several computational tools available for evaluating the stability of candidate reference genes. These tools are based on different statistical algorithms and may produce different rankings in stability within the same reference gene study. To date, the RefFinder is the only web-based tool available for comparing and evaluating housekeeping genes as candidates to be reference genes. In this tool, we integrated the four currently available computational programs (geNorm, NormFinder, BestKeeper, and the comparative ΔCt method) into a web-based tool for evaluating the stability and reliability of reference genes. According to the gene stability rankings derived from the four programs, we assigned an appropriate weight to each gene and calculated the geometric mean of weights for the final rankings. Aside from the overall ranking, a single program or combination of the four programs can be selected for evaluating the ranking of candidate reference genes. This tool has been widely used and validated by many research laboratories around the world. You may use this tool at http://www.heartcure.com.au/reffinder/ or  https://blooge.cn/RefFinder/. You can also download this algorithm program from https://github.com/fulxie/RefFinder and setup on your own computer. RefFinder is developed by PHP. Users can deploy it to a Php-based server (Apache + PHP) and run it.

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Acknowledgements

We would like to thank the authors of the four programs (geNorm, Normfinder, BestKeeper, and the comparative ΔCt method) for their agreement to allow us usage of their programs. We also greatly appreciate various web servers, such as http://www.heartcure.com.au/reffinder/ and https://blooge.cn/RefFinder/, to host the web tool for public users. RefFinder can be downloaded from https://github.com/fulxie/RefFinder and set up on your own computer and/or your own website.

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Authors and Affiliations

  1. Department of Biology, East Carolina University, Greenville, NC, 27858, USA

    Fuliang Xie & Baohong Zhang

  2. Guangxi University of Finance and Economics, Nanning, 530031, Guangxi, China

    Jianyu Wang

Authors
  1. Fuliang Xie
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  2. Jianyu Wang
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  3. Baohong Zhang
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Contributions

Fuliang Xie designed the web tool and wrote the manuscript; Jianyu Wang performed the data analysis; Baohong Zhang formed the concepts and revised the manuscript. All authors approved this manuscript.

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Correspondence to Baohong Zhang.

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Xie, F., Wang, J. & Zhang, B. RefFinder: a web-based tool for comprehensively analyzing and identifying reference genes. Funct Integr Genomics 23, 125 (2023). https://doi.org/10.1007/s10142-023-01055-7

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  • DOI: https://doi.org/10.1007/s10142-023-01055-7

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