Identification of Novel Reference Genes Based on MeSH Categories

Erşahin, Tülin; Çarkacioğlu, Levent; Can, Tolga; Konu, Özlen; Atalay, Volkan; Cetin-Atalay, Rengül

doi:10.1371/journal.pone.0093341

Cited by 15 publications

(10 citation statements)

References 28 publications

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“…This was recognized by Kwon et al ( 46 ), who selected low variability as the leading parameter, as have other studies, whereas the approach of the present study was aimed at finding genes with the best combination of criteria, considering that a high expression value may be advantageous in practice for the usability of a reference gene. Finally, it should be noted that other studies have frequently used very different and original approaches to the problem, using computational classifiers ( 47 ), the controlled vocabulary of Medical Subject Headings ( 48 ) and Gene Ontology classifications ( 29 ).…”

Section: Discussionmentioning

confidence: 99%

Systematic identification of human housekeeping genes possibly useful as references in gene expression studies

Caracausi

Piovesan

Antonaros

et al. 2017

Molecular Medicine Reports

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The ideal reference, or control, gene for the study of gene expression in a given organism should be expressed at a medium-high level for easy detection, should be expressed at a constant/stable level throughout different cell types and within the same cell type undergoing different treatments, and should maintain these features through as many different tissues of the organism. From a biological point of view, these theoretical requirements of an ideal reference gene appear to be best suited to housekeeping (HK) genes. Recent advancements in the quality and completeness of human expression microarray data and in their statistical analysis may provide new clues toward the quantitative standardization of human gene expression studies in biology and medicine, both cross- and within-tissue. The systematic approach used by the present study is based on the Transcriptome Mapper tool and exploits the automated reassignment of probes to corresponding genes, intra- and inter-sample normalization, elaboration and representation of gene expression values in linear form within an indexed and searchable database with a graphical interface recording quantitative levels of expression, expression variability and cross-tissue width of expression for more than 31,000 transcripts. The present study conducted a meta-analysis of a pool of 646 expression profile data sets from 54 different human tissues and identified actin γ 1 as the HK gene that best fits the combination of all the traditional criteria to be used as a reference gene for general use; two ribosomal protein genes, RPS18 and RPS27, and one aquaporin gene, POM121 transmembrane nucleporin C, were also identified. The present study provided a list of tissue- and organ-specific genes that may be most suited for the following individual tissues/organs: Adipose tissue, bone marrow, brain, heart, kidney, liver, lung, ovary, skeletal muscle and testis; and also provides in these cases a representative, quantitative portrait of the relative, typical gene-expression profile in the form of searchable database tables.

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Section: Discussionmentioning

confidence: 99%

Systematic identification of human housekeeping genes possibly useful as references in gene expression studies

Caracausi

Piovesan

Antonaros

et al. 2017

Molecular Medicine Reports

View full text Add to dashboard Cite

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“…MT-ATP6 was also one of the most stably-expressed control genes among 32 studied by Jones et al in eight human tissues [ 21 ]. The RPS17 , earlier described among the most stably expressed genes in carcinoma cells [ 23 ], was highly stable in control PBMCs and LCL1 (the first position in the comprehensive ranking), as well as in PBMCs of ALS and LCL2 (the second position).…”

Section: Discussionmentioning

confidence: 99%

Validation of qPCR reference genes in lymphocytes from patients with amyotrophic lateral sclerosis

et al. 2017

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Quantitative polymerase chain reaction (qPCR) is the most specific and reliable method for determination of mRNA gene expression. Crucial point for its accurate normalization is the choice of appropriate internal control genes (ICGs). In the present work we determined and compare the expression of eight commonly used ICGs in lymphocytes from 26 patients with amyotrophic lateral sclerosis (ALS) and 30 control subjects. Peripheral blood mononuclear cells (PBMCs) before and after immortalization by EBV transfection (lymphoblast cell lines—LCLs) were used for qPCR analysis. LCLs were studied before and after liquid nitrogen cryopreservation and culturing (groups LCL1 and LCL2, respectively). qPCR data of 8 ICGs expression was analyzed by BestKeeper, NormFinder and geNorm methods. All studied genes (18SRNA, ACTB, B2M, GUSB,GAPDH, HPRT1, MT-ATP6 and RPS17) were expressed in PBMCs, whereas only first four in LCLs. LCLs cryopreservation had no effect on ICGs expression. Comprehensive ranking indicated RPS17 with MT-ATP6 as the best ICGs for qPCR in PBMCs of control and ALS subjects, and RPS17 with 18RNA or MT-ATP6 in LCLs from ALS. In PBMCs 18RNA shouldn’t be used as ICG.

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“…To identify stably expressed genes in cervical cancer samples, the selection of candidates was limited to genes that have been previously reported as reference genes in the literature [ 10 , 11 , 13 , 18 , 30 – 35 ], as novel reference candidates based on meta-analysis of large-scale microarray or RNA sequencing data sets [ 19 – 23 ], or present on the TaqMan Express Human Endogenous Control Plate (Applied Biosystems). This resulted in a list of 422 different genes, for which 410 were present on the Illumina array used in the present study ( Fig 1 , S1 Table ), represented by 631 different probes.…”

Section: Resultsmentioning

confidence: 99%

“…Most studies searching for reference genes start with a limited panel of about 8–25 candidates selected on the basis of genes commonly used in the literature, which are not necessarily the most stably expressed genes. Utilizing whole genome expression data for an initial evaluation of candidates may be useful for identifying the most promising panel of genes to test in an RT-qPCR assay [ 19 – 24 ]. In the present study, this approach was used to identify suitable reference genes for hypoxia studies in cervical cancer biopsies.…”

Section: Introductionmentioning

confidence: 99%

Identification and Validation of Reference Genes for RT-qPCR Studies of Hypoxia in Squamous Cervical Cancer Patients

et al. 2016

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Hypoxia is an adverse factor in cervical cancer, and hypoxia-related gene expression could be a powerful biomarker for identifying the aggressive hypoxic tumors. Reverse transcription quantitative PCR (RT-qPCR) is a valuable method for gene expression studies, but suitable reference genes for data normalization that are independent of hypoxia status and clinical parameters of cervical tumors are lacking. In the present work, we aimed to identify reference genes for RT-qPCR studies of hypoxia in squamous cervical cancer. From 422 candidate reference genes selected from the literature, we used Illumina array-based expression profiles to identify 182 genes not affected by hypoxia in cervical cancer, i.e. genes regulated by hypoxia in eight cervical cancer cell lines or correlating with the hypoxia-associated dynamic contrast-enhanced magnetic resonance imaging parameter ABrix in 42 patients, were excluded. Among the 182 genes, nine candidates (CHCHD1, GNB2L1, IPO8, LASP1, RPL27A, RPS12, SOD1, SRSF9, TMBIM6) that were not associated with tumor volume, stage, lymph node involvement or disease progression in array data of 150 patients, were selected for further testing by RT-qPCR. geNorm and NormFinder analyses of RT-qPCR data of 74 patients identified CHCHD1, SRSF9 and TMBIM6 as the optimal set of reference genes, with stable expression both overall and across patient subgroups with different hypoxia status (ABrix) and clinical parameters. The suitability of the three reference genes were validated in studies of the hypoxia-induced genes DDIT3, ERO1A, and STC2. After normalization, the RT-qPCR data of these genes showed a significant correlation with Illumina expression (P<0.001, n = 74) and ABrix (P<0.05, n = 32), and the STC2 data were associated with clinical outcome, in accordance with the Illumina data. Thus, CHCHD1, SRSF9 and TMBIM6 seem to be suitable reference genes for studying hypoxia-related gene expression in squamous cervical cancer samples by RT-qPCR. Moreover, STC2 is a promising prognostic hypoxia biomarker in cervical cancer.

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Identification of Novel Reference Genes Based on MeSH Categories

Cited by 15 publications

References 28 publications

Systematic identification of human housekeeping genes possibly useful as references in gene expression studies

Systematic identification of human housekeeping genes possibly useful as references in gene expression studies

Validation of qPCR reference genes in lymphocytes from patients with amyotrophic lateral sclerosis

Identification and Validation of Reference Genes for RT-qPCR Studies of Hypoxia in Squamous Cervical Cancer Patients

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