ArticlePlanta2012
A critique of widely used normalization software tools and an alternative method to identify reliable reference genes in red clover (Trifolium pratense L.).
Article in Planta, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
26 citing papers in PubMed, 54 citations in OpenAlex.
- Matrix- and Differentiation Stage-Dependent Variability of Reference Genes: Rethinking Validation Strategies in 3T3-L1 Adipogenic Models.International journal of molecular sciences · 2026Article
- Effect of Savirin or Ticagrelor Treatment on the Expression of Commonly Used Reference Genes inMicroorganisms · 2023Article
- Systematic identification of reference genes for qRT-PCR ofFrontiers in plant science · 2023Article
- Validation of Appropriate Reference Genes for qRT-PCR Normalization in Oat (International journal of molecular sciences · 2022Article
- Transcription Profile of Auxin Related Genes during Positively Gravitropic Hypocotyl Curvature ofPlants (Basel, Switzerland) · 2022Article
- Normalization strategy for selection of reference genes for RT-qPCR analysis in left ventricles of failing human hearts.BMC cardiovascular disorders · 2022Article
- Reverse transcription priming methods affect normalisation choices for gene expression levels in oocytes and early embryos.Molecular human reproduction · 2021Article
- Rational, Unbiased Selection of Reference Genes for Pluripotent Stem Cell-Derived Cardiomyocytes.Tissue engineering. Part C, Methods · 2021Article
- Selection and Validation of Reference Genes for qRT-PCR Analysis in the Oil-Rich Tuber Crop Tiger Nut (International journal of molecular sciences · 2021Article
- Evaluation of micro-RNA in extracellular vesicles from blood of patients with prostate cancer.PloS one · 2021Article
- Selection and validation of reference genes for quantitative Real-Time PCR in Arabis alpina.PloS one · 2019Article
- Oral Health May Affect the Performance of mRNA-Based Saliva Biomarkers for Oral Squamous Cell Cancer.Pathology oncology research : POR · 2018Article
- Selection of reference genes for reverse transcription-qPCR analysis in the biomonitor macrophytePhysiology and molecular biology of plants : an international journal of functional plant biology · 2018Article
- Assessment of Aedes albopictus reference genes for quantitative PCR at different stages of development.PloS one · 2018Article
- Evaluation of reference genes at different developmental stages for quantitative real-time PCR in Aedes aegypti.Scientific reports · 2017Article
- Selection of suitable reference genes for gene expression studies in Staphylococcus capitis during growth under erythromycin stress.Molecular genetics and genomics : MGG · 2016Article
- Identification of suitable grapevine reference genes for qRT-PCR derived from heterologous species.Molecular genetics and genomics : MGG · 2016Article
- Evaluation of Reference Genes for Quantitative Real-Time PCR Analysis of the Gene Expression in Laticifers on the Basis of Latex Flow in Rubber Tree (Hevea brasiliensis Muell. Arg.).Frontiers in plant science · 2016Article
- Gene expression profiling of candidate virulence factors in the laminated root rot pathogen Phellinus sulphurascens.BMC genomics · 2014Article
- Profiling Gene Expression in GerminatingPlant molecular biology reporter · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Determination of appropriate reference genes is crucial to normalization of gene expression data and prevention of biased results in qRT-PCR studies. This study is the first attempt to systematically compare potential reference genes to detect the most constitutively expressed reference genes for accurate normalization in red clover tissues including leaves, stems and roots. To identify the best-suited reference gene(s) for normalization, several statistical algorithms such as geNorm, BestKeeper and NormFinder have been developed. All these algorithms are based on the key assumption that none of the investigated candidate reference genes show systematic variation in their expression profile across the samples being considered. However, this assumption is likely to be violated in practice. The authors therefore suggest a simple and novel stability index based on the analysis of variance model which is free from the assumption made by the algorithms. We assessed the expression stability of eight candidate reference genes including actin (ACT), glyceraldehyde-3-phosphate-dehydrogenase (GADPH), elongation factor-1alpha (EF-1α), translation initiation factor (EIF-4a), ubiquitin-conjugating enzyme E2 (UBC2), polyubiquitin (UBQ10), sand family protein (SAND) and yellow-leaf-specific protein 8 (YLS8). Our results indicated that UBC2 and UBQ10 ranked as the two most stably expressed genes in leaf tissue. UBC2 and YLS8 were defined as optimal control genes for stem tissue. EIF-4a and UBC2 were found to be the most stable reference gene for root tissue. GAPDH and SAND showed relatively low stability in expression study of red clover. When all tested tissues were considered, we observed that YLS8 and UBC2 showed remarkable stability in their expression level across tissues.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.