IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0021012.html
   My bibliography  Save this article

Predicting Housekeeping Genes Based on Fourier Analysis

Author

Listed:
  • Bo Dong
  • Peng Zhang
  • Xiaowei Chen
  • Li Liu
  • Yunfei Wang
  • Shunmin He
  • Runsheng Chen

Abstract

Housekeeping genes (HKGs) generally have fundamental functions in basic biochemical processes in organisms, and usually have relatively steady expression levels across various tissues. They play an important role in the normalization of microarray technology. Using Fourier analysis we transformed gene expression time-series from a Hela cell cycle gene expression dataset into Fourier spectra, and designed an effective computational method for discriminating between HKGs and non-HKGs using the support vector machine (SVM) supervised learning algorithm which can extract significant features of the spectra, providing a basis for identifying specific gene expression patterns. Using our method we identified 510 human HKGs, and then validated them by comparison with two independent sets of tissue expression profiles. Results showed that our predicted HKG set is more reliable than three previously identified sets of HKGs.

Suggested Citation

  • Bo Dong & Peng Zhang & Xiaowei Chen & Li Liu & Yunfei Wang & Shunmin He & Runsheng Chen, 2011. "Predicting Housekeeping Genes Based on Fourier Analysis," PLOS ONE, Public Library of Science, vol. 6(6), pages 1-11, June.
    • Handle: RePEc:plo:pone00:0021012
    DOI: 10.1371/journal.pone.0021012
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0021012
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0021012&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0021012?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Hendrik J M de Jonge & Rudolf S N Fehrmann & Eveline S J M de Bont & Robert M W Hofstra & Frans Gerbens & Willem A Kamps & Elisabeth G E de Vries & Ate G J van der Zee & Gerard J te Meerman & Arja ter, 2007. "Evidence Based Selection of Housekeeping Genes," PLOS ONE, Public Library of Science, vol. 2(9), pages 1-5, September.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Lieven Thorrez & Katrijn Van Deun & Léon-Charles Tranchevent & Leentje Van Lommel & Kristof Engelen & Kathleen Marchal & Yves Moreau & Iven Van Mechelen & Frans Schuit, 2008. "Using Ribosomal Protein Genes as Reference: A Tale of Caution," PLOS ONE, Public Library of Science, vol. 3(3), pages 1-8, March.
    2. Florian R L Meyer & Heinrich Grausgruber & Claudia Binter & Georg E Mair & Christian Guelly & Claus Vogl & Ralf Steinborn, 2013. "Cross-Platform Microarray Meta-Analysis for the Mouse Jejunum Selects Novel Reference Genes with Highly Uniform Levels of Expression," PLOS ONE, Public Library of Science, vol. 8(5), pages 1-15, May.
    3. Wei-Chung Cheng & Cheng-Wei Chang & Chaang-Ray Chen & Min-Lung Tsai & Wun-Yi Shu & Chia-Yang Li & Ian C Hsu, 2011. "Identification of Reference Genes across Physiological States for qRT-PCR through Microarray Meta-Analysis," PLOS ONE, Public Library of Science, vol. 6(2), pages 1-8, February.
    4. Yijuan Zhang & Ding Li & Bingyun Sun, 2015. "Do Housekeeping Genes Exist?," PLOS ONE, Public Library of Science, vol. 10(5), pages 1-22, May.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0021012. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.