Identification of Reference Genes across Physiological States for qRT-PCR through Microarray Meta-Analysis
Publication Date
February 24, 2011
Journal
PLoS ONE
Authors
Wei-Chung Cheng, Cheng-Wei Chang, Chaang-Ray Chen, Min-Lung Tsai, et al
Volume
6
Issue
2
Pages
e17347
DOI
https://dx.plos.org/10.1371/journal.pone.0017347
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0017347
Web of Science
000287761700048
Scopus
79952078513
Mendeley
http://www.mendeley.com/research/identification-reference-genes-across-physiological-states-qrtpcr-through-microarray-metaanalysis
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Mendeley | Further Information

{"title"=>"Identification of reference genes across physiological states for qRT-PCR through microarray meta-analysis", "type"=>"journal", "authors"=>[{"first_name"=>"Wei Chung", "last_name"=>"Cheng", "scopus_author_id"=>"55248902800"}, {"first_name"=>"Cheng Wei", "last_name"=>"Chang", "scopus_author_id"=>"57198745856"}, {"first_name"=>"Chaang Ray", "last_name"=>"Chen", "scopus_author_id"=>"35214649200"}, {"first_name"=>"Min Lung", "last_name"=>"Tsai", "scopus_author_id"=>"35277658500"}, {"first_name"=>"Wun Yi", "last_name"=>"Shu", "scopus_author_id"=>"15053695800"}, {"first_name"=>"Chia Yang", "last_name"=>"Li", "scopus_author_id"=>"26647541400"}, {"first_name"=>"Ian C.", "last_name"=>"Hsu", "scopus_author_id"=>"7101869592"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"79952078513", "doi"=>"10.1371/journal.pone.0017347", "pui"=>"361341365", "pmid"=>"21390309", "scopus"=>"2-s2.0-79952078513", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"23975e90-aa32-3d4a-9f25-e8e70269f80a", "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.\\n\\nMETHODOLOGY/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.\\n\\nCONCLUSIONS/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.", "link"=>"http://www.mendeley.com/research/identification-reference-genes-across-physiological-states-qrtpcr-through-microarray-metaanalysis", "reader_count"=>40, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Student > Doctoral Student"=>3, "Researcher"=>13, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>2, "Student > Master"=>5, "Student > Bachelor"=>5, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Student > Doctoral Student"=>3, "Researcher"=>13, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>2, "Student > Master"=>5, "Student > Bachelor"=>5, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>4, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Medicine and Dentistry"=>9, "Agricultural and Biological Sciences"=>22, "Neuroscience"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>4}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>9}, "Neuroscience"=>{"Neuroscience"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>22}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Austria"=>1, "United States"=>3, "France"=>1, "Australia"=>1, "Chile"=>1, "Germany"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/398003", "https://ndownloader.figshare.com/files/398033", "https://ndownloader.figshare.com/files/398077"], "description"=>"<div><h3>Background</h3><p>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.</p> <h3>Methodology/Principal Findings</h3><p>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.</p> <h3>Conclusions/Significance</h3><p>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.</p> </div>", "links"=>[], "tags"=>["genes", "physiological", "states", "for", "qrt-pcr", "microarray", "meta-analysis"], "article_id"=>138637, "categories"=>["Biological Sciences"], "users"=>["Wei-Chung Cheng", "Cheng-Wei Chang", "Chaang-Ray Chen", "Min-Lung Tsai", "Wun-Yi Shu", "Chia-Yang Li", "Ian C. Hsu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0017347.s001", "https://dx.doi.org/10.1371/journal.pone.0017347.s002", "https://dx.doi.org/10.1371/journal.pone.0017347.s003"], "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Identification_of_Reference_Genes_across_Physiological_States_for___qRT_PCR_through_Microarray_Meta_Analysis/138637", "title"=>"Identification of Reference Genes across Physiological States for\n qRT-PCR through Microarray Meta-Analysis", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-02-24 02:23:57"}
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  • {"files"=>["https://ndownloader.figshare.com/files/795966"], "description"=>"<p>*The criterion is that the CV of the intensity of the gene in the\n physiological state is smaller than 30%. CV, coefficient of\n variation, is equal to standard deviation divided by mean.</p>§<p>The criterion is that the maximum of the fold change of mean\n intensity between physiological states is smaller than 1.2.</p>¥<p>The number of genes stably expressed within and between physiological\n states.</p>", "links"=>[], "tags"=>["genes", "passed", "13"], "article_id"=>466332, "categories"=>["Biological Sciences"], "users"=>["Wei-Chung Cheng", "Cheng-Wei Chang", "Chaang-Ray Chen", "Min-Lung Tsai", "Wun-Yi Shu", "Chia-Yang Li", "Ian C. Hsu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017347.t002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_the_number_of_genes_passed_different_criteria_in_13____organ_tissue_types_/466332", "title"=>"Summary of the number of genes passed different criteria in 13\n organ/tissue types.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-02-24 01:45:32"}
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  • {"files"=>["https://ndownloader.figshare.com/files/796011"], "description"=>"<p>fRGs and the corresponding numbers of organ/tissue types for which\n fRGs were identified.</p>", "links"=>[], "tags"=>["corresponding", "numbers", "types", "which", "frgs"], "article_id"=>466373, "categories"=>["Biological Sciences"], "users"=>["Wei-Chung Cheng", "Cheng-Wei Chang", "Chaang-Ray Chen", "Min-Lung Tsai", "Wun-Yi Shu", "Chia-Yang Li", "Ian C. Hsu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017347.t003", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_fRGs_and_the_corresponding_numbers_of_organ_tissue_types_for_which____fRGs_were_identified_/466373", "title"=>"fRGs and the corresponding numbers of organ/tissue types for which\n fRGs were identified.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-02-24 01:46:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/795754"], "description"=>"<p>The upper and lower halfs of the figure are 6 fRGs and 6 tRGs\n respectively. The error bar is the standard deviation of intensity.\n * denotes the gene identified as RG in the organ/tissue type.</p>", "links"=>[], "tags"=>["profiles", "trgs", "frgs", "physiological", "states", "13"], "article_id"=>466116, "categories"=>["Biological Sciences"], "users"=>["Wei-Chung Cheng", "Cheng-Wei Chang", "Chaang-Ray Chen", "Min-Lung Tsai", "Wun-Yi Shu", "Chia-Yang Li", "Ian C. Hsu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017347.g002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_profiles_of_6_tRGs_and_6_fRGs_for_4_physiological_states____in_13_organ_tissue_types_/466116", "title"=>"Expression profiles of 6 tRGs and 6 fRGs for 4 physiological states\n in 13 organ/tissue types.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-02-24 01:41:56"}

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Relative Metric

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