Journal of Periodontal and Implant Science

Korean Academy of Periodontology (대한치주과학회)
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Reliability of microarray analysis for studying periodontitis: low consistency in 2 periodontitis cohort data sets from different platforms and an integrative meta-analysis

  • Jeon, Yoon-Seon (Department of Periodontology, Research Institute for Periodontal Regeneration, Yonsei University College of Dentistry) ;
  • Shivakumar, Manu (Department of Biostatistics, Epidemiology and Informatics, The Perelman School of Medicine, University of Pennsylvania) ;
  • Kim, Dokyoon (Department of Biostatistics, Epidemiology and Informatics, The Perelman School of Medicine, University of Pennsylvania) ;
  • Kim, Chang-Sung (Department of Periodontology, Research Institute for Periodontal Regeneration, Yonsei University College of Dentistry) ;
  • Lee, Jung-Seok (Department of Periodontology, Research Institute for Periodontal Regeneration, Yonsei University College of Dentistry)
  • Received : 2020.03.30
  • Accepted : 2020.09.24
  • Published : 2021.02.28
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Abstract

Purpose: The aim of this study was to compare the characteristic expression patterns of advanced periodontitis in 2 cohort data sets analyzed using different microarray platforms, and to identify differentially expressed genes (DEGs) through a meta-analysis of both data sets. Methods: Twenty-two patients for cohort 1 and 40 patients for cohort 2 were recruited with the same inclusion criteria. The 2 cohort groups were analyzed using different platforms: Illumina and Agilent. A meta-analysis was performed to increase reliability by removing statistical differences between platforms. An integrative meta-analysis based on an empirical Bayesian methodology (ComBat) was conducted. DEGs for the integrated data sets were identified using the limma package to adjust for age, sex, and platform and compared with the results for cohorts 1 and 2. Clustering and pathway analyses were also performed. Results: This study detected 557 and 246 DEGs in cohorts 1 and 2, respectively, with 146 and 42 significantly enriched gene ontology (GO) terms. Overlapping between cohorts 1 and 2 was present in 59 DEGs and 18 GO terms. However, only 6 genes from the top 30 enriched DEGs overlapped, and there were no overlapping GO terms in the top 30 enriched pathways. The integrative meta-analysis detected 34 DEGs, of which 10 overlapped in all the integrated data sets of cohorts 1 and 2. Conclusions: The characteristic expression pattern differed between periodontitis and the healthy periodontium, but the consistency between the data sets from different cohorts and metadata was too low to suggest specific biomarkers for identifying periodontitis.

Keywords

Acknowledgement

This study was supported by the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT & Future Planning (grant No. NRF-2019R1A2C4069942).

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