RefFinder
2020.10.20 - 2023.12.01

Evaluating Reference Genes Expression>>
RefFinder is a user-friendly web-based comprehensive tool developed for evaluating and screening reference genes from extensive experimental datasets. It integrates the currently available major computational programs (geNorm, Normfinder, BestKeeper, and the comparative Δ-Ct method) to compare and rank the tested candidate reference genes. Based on the rankings from each program, It assigns an appropriate weight to an individual gene and calculated the geometric mean of their weights for the overall final ranking. LIZhen ( ORCID: 0000-0002-8512-2554 ) established and maintained the RefFinder mirror site ( http://blooge.cn/RefFinder/ ). Please thanks for LIZhen ( Sichuan Academy of Agricultural Characteristic Plants ) contributed analytical tool : RefFinder ( http://blooge.cn/RefFinder/ ) in Acknowledgements or Contributions ( just like DOI: 10.1007/s10142-023-01055-7 , 10.1038/s41598-022-16124-3 , 10.3389/fmicb.2023.1140515 , 10.3390/biomedicines11041079 , 10.1016/j.tox.2023.153678 ) .
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References
  1. RefFinder ( DOI: 10.1007/s11103-012-9885-2 (2012) , 10.1007/s10142-023-01055-7 (2023) )
    Added at the request of the RefFinder author Baohong Zhang
    "If you employed RefFinder for your study, please cite the following papers: Xie, F., Wang, J. & Zhang, B. RefFinder: a web-based tool for comprehensively analyzing and identifying reference genes. Funct Integr Genomics 23, 125 (2023). DOI: 10.1007/s10142-023-01055-7 and Xie, F., Xiao, P., Chen, D. et al. miRDeepFinder: a miRNA analysis tool for deep sequencing of plant small RNAs. Plant Mol Biol 80, 75–84 (2012). DOI: 10.1007/s11103-012-9885-2"
    Please respect copyright
  2. Genorm ( DOI: 10.1186/gb-2002-3-7-research0034 )
  3. NormFinder ( DOI: 10.1158/0008-5472.can-04-0496 )
  4. BestKeeper ( DOI: 10.1023/b:bile.0000019559.84305.47 )
  5. The comparative delta-Ct method ( DOI: 10.1186/1471-2199-7-33 )
Citations
    RefFinder ( http://blooge.cn/RefFinder/ )
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      Assessment of reference genes at six different developmental stages of Schistosoma mansoni for quantitative RT-PCR
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      Evaluation of Reliable Reference Genes for In Vitro Erythrocyte Generation from Cord Blood CD34+ Cells
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      Identification of Reference Genes for Reverse Transcription-Quantitative PCR Analysis of Ginger Under Abiotic Stress and for Postharvest Biology Studies
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      Selection and Validation of Reference Genes for Gene Expression Studies Using Quantitative Real-Time PCR in Prunus Necrotic Ringspot Virus-Infected Cucumis sativus
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      Validation of reference genes for gene expression analysis in fruit development of Vaccinium bracteatum Thunb using quantitative real-time PCR
      ------------------ ↑ IF2020 ↑ ------------------ ↓ IF2021 ↓ ------------------
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      Identification of Reference Genes for RT-qPCR Analysis in Gleditsia microphylla under Abiotic Stress and Hormone Treatment
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      Trypsin is a coordinate regulator of N and P nutrients in marine phytoplankton
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      Identification of internal reference genes for porcine immature Sertoli cells under heat stress
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      Systematic screening and validation of reliable reference genes for qRT-PCR analysis in Okra (Abelmoschus esculentus L.)
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      Co-overexpression of self-renewal markers SALL4 and HIWI is correlated with depth of tumor invasion and metastasis in colorectal cancer
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      Nutrient Starvation Exposure Induced the Down-Regulation of Stress Responsive Genes and Selected Bioactive Metabolic Pathways in Phaeodactylum tricornutum
    37. 20220826　DOI: 10.3390/insects13090773　Insects （IF=3.139）
      Assessment of Suitable Reference Genes for qRT-PCR Normalization in Eocanthecona furcellata (Wolff)
    38. 20220830　CN114958875A　中国专利
      柑橘黄龙病菌内参基因metG筛选和应用
    39. 20220923　DOI: 10.3390/ijms231911187　International Journal of Molecular Sciences （IF=6.208）
      Validation of Appropriate Reference Genes for qRT–PCR Normalization in Oat (Avena sativa L.) under UV-B and High-Light Stresses
    40. 20221009　DOI: 10.1038/s41598-022-20864-7　Scientific Reports （IF=4.996）
      Validation of reference genes for gene expression analysis in fruit development of Vaccinium bracteatum Thunb. using quantitative real-time PCR
    41. 20221017　DOI: 10.7717/peerj.14221　Peer J （IF=3.061）
      Comparison of reference gene expression stability in mouse skeletal muscle via five algorithms
    42. 20221018　DOI: 10.1093/jee/toac162　Journal of Economic Entomology （IF=2.447）
      Selection of Reference Genes for Normalization of qRT‒PCR Analysis in the Soybean Aphid Aphis glycines Matsumura (Hemiptera: Aphididae)
    43. 20221019　DOI: 10.3389/fphys.2022.1046204　Frontiers in Physiology （IF=4.755）
      Selection and validation of reference genes for RT-qPCR-based analyses of Anastatus japonicus Ashmead (Hymenoptera: Helicopteridae)
    44. 20221024　DOI: 10.21203/rs.3.rs-2119629/v1　Research Square （preprint）
      Evaluation of housekeeping genes for normalizing RT-qPCR and analysis of the expression patterns of WRKY1 transcription factor and rhynchophylline biosynthetic-related genes in Uncaria rhynchophylla
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      Systematic Identification and Validation of Suitable Reference Genes for the Normalization of Gene Expression in Prunella vulgaris under Different Organs and Spike Development Stages
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      circSMARCA5 Is an Upstream Regulator of the Expression of miR-126-3p, miR-515-5p, and Their mRNA Targets, Insulin-like Growth Factor Binding Protein 2 (IGFBP2) and NRAS Proto-Oncogene, GTPase (NRAS) in Glioblastoma
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      Reference Genes for Expression Analysis Using RT-qPCR in Cnaphalocrocis medinalis (Lepidoptera: Pyralidae)
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      条沙叶蝉 Psammotettix striatus 马氏管功能和体表网粒体研究
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      钩藤管家基因筛选及生物碱合成相关基因的表达分析
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      奶牛乳脂代谢关键基因、LncRNAs的筛选及PI4K2A功能验证
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      Identification of Reliable Reference Genes under Different Stresses and in Different Tissues of Toxicodendron succedaneum
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      Evaluation of Reference Genes Suitable for Gene Expression during Root Enlargement in Cherry Radish Based on Transcriptomic Data
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      DNA methylation dynamics in a coastal foundation seagrass species under abiotic stressors
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      Selection and Validation of miRNA Reference Genes by Quantitative Real-Time PCR Analysis in Paeonia suffruticosa
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      Identification of reference genes for RT-qPCR analysis across kiwifruit species under iron deficiency conditions
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      circRNA432 enhances the coelomocyte phagocytosis via regulating the miR-2008-ELMO1 axis in Vibrio splendidus-challenged Apostichopus japonicus
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      基于全基因组鉴定华石斛优良内参基因
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      Evaluation of Candidate Reference Genes for Gene Expression Analysis in Wild Lamiophlomis rotata
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      Transcriptome-Based Evaluation of Optimal Reference Genes for Quantitative Real-Time PCR in Yak Stomach throughout the Growth Cycle
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      Quantitative evaluation of endogenous reference genes for ddPCR under salt stress using a moderate halophile
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      Evaluation of reference genes for transcript analyses in Komagataella phaffii (Pichia pastoris)
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      镉胁迫下构树qRT-PCR内参基因筛选及验证
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      滇重楼和长柱重楼实时荧光定量PCR内参基因的筛选和验证
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      野皂荚内参基因及性别相关基因的克隆与鉴定
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      A Strategy for the Selection of RT-qPCR Reference Genes Based on Publicly Available Transcriptomic Datasets
    74. 20230413　DOI: 10.1007/s12600-023-01068-9　Phytoparasitica （IF=1.809）
      Callose synthase and xyloglucan endotransglucosylase gene expression over time in Citrus × clementina and Citrus × sinensis infected with citrus tristeza virus
    75. 20230415　DOI: 10.1007/s10142-023-01055-7　Functional & Integrative Genomics （IF=3.674）
      RefFinder: a web-based tool for comprehensively analyzing and identifying reference genes
    76. 20230418　DOI: 10.21203/rs.3.rs-2750081/v1　Research Square （preprint）
      Immune Response to Zinc Oxide Inhalation in Metal Fume Fever - Is the IL-17f the missing link?
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      梨小食心虫实时荧光定量PCR内参基因的筛选
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      Stable reference gene selection for Ophiocordyceps sinensis gene expression studies under different developmental stages and light-induced conditions
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      Identification of reference genes for the normalization of retinal mRNA expression by RT-qPCR in oxygen induced retinopathy, anemia, and erythropoietin administration
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      Direct BMP signaling to chordoblasts is required for the initiation of segmented notochord sheath mineralization in zebrafish vertebral column development
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      Transcriptomics and physiological analyses unveil the distinct mechanisms of ATP and glucose-6-phosphate utilization in Phaeodactylum tricornutum
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      Identification and Validation of Reference Genes for Expression Analysis Using RT-qPCR in Leptocybe invasa Fisher and La Salle (Hymenoptera: Eulophidae)
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      PFOA exposure induces aberrant glucose and lipid metabolism in the rat liver through the AMPK/mTOR pathway
    88. 20230525　DOI: 10.3390/app13116489　Applied Sciences （IF=2.838）
      Antidiabetic and Hypolipidemic Properties of Newly Isolated Wild Lacticaseibacillus paracasei Strains in Mature Adipocytes
    89. 20230531　DOI: 10.3390/plants12112185　Plants （IF=4.658）
      Selection and Validation of Optimal RT-qPCR Reference Genes for the Normalization of Gene Expression under Different Experimental Conditions in Lindera megaphylla
    90. 20230601　DOI: 10.1097/FJC.0000000000001428　Journal of Cardiovascular Pharmacology （IF=3.271）
      Tumor Necrosis Factor-α Mediates Inflammation-induced Early-Stage Left Ventricular Systolic Dysfunction
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      实时荧光定量PCR筛选镉胁迫下艾纳香(Blumea balsamifera DC.)的内参基因
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      Maternal diet and gut microbiome composition modulate early-life immune development
    93. 20230619　DOI: 10.1007/s12298-023-01325-5　Physiology and Molecular Biology of Plants （IF=3.023）
      Selection and verification of reliable internal reference genes in stem development of herbaceous peony (Paeonia lactiflora Pall.)
    94. 20230623　DOI: 10.3390/genes14071321　Genes （IF=4.141）
      Selection of Reliable Reference Genes for Gene Expression Normalization in Sagittaria trifolia
      ------------------ ↑ IF2021 ↑ ------------------ ↓ IF2022 ↓ ------------------
    95. 20230629　DOI: 10.3390/ijms241310884　International Journal of Molecular Sciences （IF=5.6）
      Data Normalization of Urine miRNA Profiling from Head and Neck Cancer Patients Treated with Cisplatin
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      Identification of reference genes provides insights into the determinants of self-incompatibility in Camellia oleifera
    97. 20230712　DOI: 10.3390/plants12142629　Plants （IF=4.5）
      Screening of Reference miRNA of Different Early- and Late-Flowering Tree Peony Varieties
    98. 20230720　DOI: 10.3390/antiox12071462　Antioxidants （IF=7.0）
      High-Intensity Exercise Promotes Deleterious Cardiovascular Remodeling in a High-Cardiovascular-Risk Model: A Role for Oxidative Stress
    99. 20230807　DOI: 10.19540/j.cnki.cjcmm.20230726.101　中国中药杂志 （中文）
      川赤芍实时荧光定量PCR内参基因的筛选与验证
    100. 20230811　DOI: 10.3389/fncel.2023.1225504　Frontiers in Cellular Neuroscience （IF=5.3）
      Regeneration of the cerebral cortex by direct chemical reprogramming of macrophages into neuronal cells in acute ischemic stroke
    101. 20230825　DOI: 10.1021/acs.jafc.3c04247　Journal of Agricultural and Food Chemistry （IF=6.1）
      Loss of Binding Capabilities in an Ecologically Important Odorant Receptor of the Fall Armyworm, Spodoptera frugiperda, by a Single Point Mutation
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      Genome-wide analysis of Panonychus citri microRNAs with a focus on potential insecticidal activity of 4 microRNAs to eggs and nymphs
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      Validation of reference gene stability for miRNA quantification by reverse transcription quantitative PCR in the peripheral blood of patients with COVID-19 critical illness
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