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Identification of Human Housekeeping Genes and Tissue-Selective Genes by Microarray Meta-Analysis

Author

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

Abstract

Background: Categorizing protein-encoding transcriptomes of normal tissues into housekeeping genes and tissue-selective genes is a fundamental step toward studies of genetic functions and genetic associations to tissue-specific diseases. Previous studies have been mainly based on a few data sets with limited samples in each tissue, which restrained the representativeness of their identified genes, and resulted in low consensus among them. Results: This study compiled 1,431 samples in 43 normal human tissues from 104 microarray data sets. We developed a new method to improve gene expression assessment, and showed that more than ten samples are needed to robustly identify the protein-encoding transcriptome of a tissue. We identified 2,064 housekeeping genes and 2,293 tissue-selective genes, and analyzed gene lists by functional enrichment analysis. The housekeeping genes are mainly involved in fundamental cellular functions, and the tissue-selective genes are strikingly related to functions and diseases corresponding to tissue-origin. We also compared agreements and related functions among our housekeeping genes and those of previous studies, and pointed out some reasons for the low consensuses. Conclusions: The results indicate that sufficient samples have improved the identification of protein-encoding transcriptome of a tissue. Comprehensive meta-analysis has proved the high quality of our identified HK and TS genes. These results could offer a useful resource for future research on functional and genomic features of HK and TS genes.

Suggested Citation

  • 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.
    • Handle: RePEc:plo:pone00:0022859
    DOI: 10.1371/journal.pone.0022859
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    References listed on IDEAS

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    1. Adaikalavan Ramasamy & Adrian Mondry & Chris C Holmes & Douglas G Altman, 2008. "Key Issues in Conducting a Meta-Analysis of Gene Expression Microarray Datasets," PLOS Medicine, Public Library of Science, vol. 5(9), pages 1-13, September.
    2. 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.
    3. Hector Sandoval & Perumal Thiagarajan & Swapan K. Dasgupta & Armin Schumacher & Josef T. Prchal & Min Chen & Jin Wang, 2008. "Essential role for Nix in autophagic maturation of erythroid cells," Nature, Nature, vol. 454(7201), pages 232-235, July.
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    Cited by:

    1. Yijuan Zhang & Ding Li & Bingyun Sun, 2015. "Do Housekeeping Genes Exist?," PLOS ONE, Public Library of Science, vol. 10(5), pages 1-22, May.

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