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

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 f...

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Autores principales: Cheng, Wei-Chung, Chang, Cheng-Wei, Chen, Chaang-Ray, Tsai, Min-Lung, Shu, Wun-Yi, Li, Chia-Yang, Hsu, Ian C.
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044736/
https://www.ncbi.nlm.nih.gov/pubmed/21390309
http://dx.doi.org/10.1371/journal.pone.0017347
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author Cheng, Wei-Chung
Chang, Cheng-Wei
Chen, Chaang-Ray
Tsai, Min-Lung
Shu, Wun-Yi
Li, Chia-Yang
Hsu, Ian C.
author_facet Cheng, Wei-Chung
Chang, Cheng-Wei
Chen, Chaang-Ray
Tsai, Min-Lung
Shu, Wun-Yi
Li, Chia-Yang
Hsu, Ian C.
author_sort Cheng, Wei-Chung
collection PubMed
description 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.
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spelling pubmed-30447362011-03-09 Identification of Reference Genes across Physiological States for qRT-PCR through Microarray Meta-Analysis Cheng, Wei-Chung Chang, Cheng-Wei Chen, Chaang-Ray Tsai, Min-Lung Shu, Wun-Yi Li, Chia-Yang Hsu, Ian C. PLoS One Research Article 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. Public Library of Science 2011-02-24 /pmc/articles/PMC3044736/ /pubmed/21390309 http://dx.doi.org/10.1371/journal.pone.0017347 Text en Cheng et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Cheng, Wei-Chung
Chang, Cheng-Wei
Chen, Chaang-Ray
Tsai, Min-Lung
Shu, Wun-Yi
Li, Chia-Yang
Hsu, Ian C.
Identification of Reference Genes across Physiological States for qRT-PCR through Microarray Meta-Analysis
title Identification of Reference Genes across Physiological States for qRT-PCR through Microarray Meta-Analysis
title_full Identification of Reference Genes across Physiological States for qRT-PCR through Microarray Meta-Analysis
title_fullStr Identification of Reference Genes across Physiological States for qRT-PCR through Microarray Meta-Analysis
title_full_unstemmed Identification of Reference Genes across Physiological States for qRT-PCR through Microarray Meta-Analysis
title_short Identification of Reference Genes across Physiological States for qRT-PCR through Microarray Meta-Analysis
title_sort identification of reference genes across physiological states for qrt-pcr through microarray meta-analysis
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044736/
https://www.ncbi.nlm.nih.gov/pubmed/21390309
http://dx.doi.org/10.1371/journal.pone.0017347
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