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Identification of Reference Genes across Physiological States for qRT-PCR through Microarray Meta-Analysis

Author

Listed:
  • Wei-Chung Cheng
  • Cheng-Wei Chang
  • Chaang-Ray Chen
  • Min-Lung Tsai
  • Wun-Yi Shu
  • Chia-Yang Li
  • Ian C Hsu

Abstract

Background: The accuracy of quantitative real-time PCR (qRT-PCR) is highly dependent on reliable reference gene(s). Some housekeeping genes which are commonly used for normalization are widely recognized as inappropriate in many experimental conditions. This study aimed to identify reference genes for clinical studies through microarray meta-analysis of human clinical samples. Methodology/Principal Findings: After uniform data preprocessing and data quality control, 4,804 Affymetrix HU-133A arrays performed by clinical samples were classified into four physiological states with 13 organ/tissue types. We identified a list of reference genes for each organ/tissue types which exhibited stable expression across physiological states. Furthermore, 102 genes identified as reference gene candidates in multiple organ/tissue types were selected for further analysis. These genes have been frequently identified as housekeeping genes in previous studies, and approximately 71% of them fall into Gene Expression (GO:0010467) category in Gene Ontology. Conclusions/Significance: Based on microarray meta-analysis of human clinical sample arrays, we identified sets of reference gene candidates for various organ/tissue types and then examined the functions of these genes. Additionally, we found that many of the reference genes are functionally related to transcription, RNA processing and translation. According to our results, researchers could select single or multiple reference gene(s) for normalization of qRT-PCR in clinical studies.

Suggested Citation

  • 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.
    • Handle: RePEc:plo:pone00:0017347
    DOI: 10.1371/journal.pone.0017347
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    References listed on IDEAS

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    Cited by:

    1. 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.
    2. Cheng-Wei Chang & Wei-Chung Cheng & Chaang-Ray Chen & Wun-Yi Shu & Min-Lung Tsai & Ching-Lung Huang & Ian C Hsu, 2011. "Identification of Human Housekeeping Genes and Tissue-Selective Genes by Microarray Meta-Analysis," PLOS ONE, Public Library of Science, vol. 6(7), pages 1-10, July.

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