ArticlePloS one2008
Using ribosomal protein genes as reference: a tale of caution.
Article in PloS one, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 124 papers, 2 of them syntheses that pooled it.
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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.
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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.
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Who cites it
124 citing papers in PubMed, 2 syntheses or guidelines pooled it, 220 citations in OpenAlex.
- Deep learning and genome-wide association meta-analyses of bone marrow adiposity in the UK Biobank.Nature communications · 2025Pooled it
- Identification of reference genes across physiological states for qRT-PCR through microarray meta-analysis.PloS one · 2011Pooled it
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- Ribosome heterogeneity and specialization in musculoskeletal physiology and pathology.JBMR plus · 2026Article
- Identification of best housekeeping gene for normalization in qRT-PCR data under different development stages and stress conditions in Vigna mungo.Scientific reports · 2025Article
- HTSinfer: inferring metadata from bulk Illumina RNA-Seq libraries.Bioinformatics (Oxford, England) · 2025Article
- Gene Set Enrichment Analysis in Zebrafish Embryos Is Susceptible to False-Positive Results in the Absence of Differentially Expressed Genes.Bioinformatics and biology insights · 2025Article
- Insights into the evolution and regulation of miRNAs from the view of their DNA replication temporal domains.Frontiers in genetics · 2025Article
- High-dimensional co-expression network analysis reveals persistent TRH gene expression throughout axolotl telencephalon regeneration.Frontiers in bioinformatics · 2025Article
- Evaluation of Reference Gene Stability in Goat Skeletal Muscle Satellite Cells during Proliferation and Differentiation Phases.Animals : an open access journal from MDPI · 2024Article
- Deletion of Hsd11b1 suppresses caloric restriction-induced bone marrow adiposity in male but not female mice.The Journal of endocrinology · 2024Article
- Function and Regulation of Bone Marrow Adipose Tissue in Health and Disease: State of the Field and Clinical Considerations.Comprehensive Physiology · 2024Review
- Pathological mutations reveal the key role of the cytosolic iRhom2 N-terminus for phosphorylation-independent 14-3-3 interaction and ADAM17 binding, stability, and activity.Cellular and molecular life sciences : CMLS · 2024Article
- Long non-coding RNA-derived peptides are immunogenic and drive a potent anti-tumour response.Nature communications · 2023Article
- Chordin-like 1, a Novel Adipokine, Markedly Promotes Adipogenesis and Lipid Accumulation.Cells · 2023Article
- Identification and validation of reference genes for normalization of gene expression analysis using qRT-PCR inFrontiers in physiology · 2023Article
- Biology-inspired data-driven quality control for scientific discovery in single-cell transcriptomics.Genome biology · 2022Article
- c-MAF coordinates enterocyte zonation and nutrient uptake transcriptional programs.The Journal of experimental medicine · 2022Article
- Reference genes for the developing mouse lung under consideration of biological, technical and experimental confounders.Scientific reports · 2022Article
64 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHousekeeping genes are needed in every tissue as their expression is required for survival, integrity or duplication of every cell. Housekeeping genes commonly have been used as reference genes to normalize gene expression data, the underlying assumption being that they are expressed in every cell type at approximately the same level. Often, the terms "reference genes" and "housekeeping genes" are used interchangeably. In this paper, we would like to distinguish between these terms. Consensus is growing that housekeeping genes which have traditionally been used to normalize gene expression data are not good reference genes. Recently, ribosomal protein genes have been suggested as reference genes based on a meta-analysis of publicly available microarray data. METHODOLOGY/PRINCIPAL
findingsWe have applied several statistical tools on a dataset of 70 microarrays representing 22 different tissues, to assess and visualize expression stability of ribosomal protein genes. We confirmed the housekeeping status of these genes, but further estimated expression stability across tissues in order to assess their potential as reference genes. One- and two-way ANOVA revealed that all ribosomal protein genes have significant expression variation across tissues and exhibit tissue-dependent expression behavior as a group. Via multidimensional unfolding analysis, we visualized this tissue-dependency. In addition, we explored mechanisms that may cause tissue dependent effects of individual ribosomal protein genes. CONCLUSIONS/SIGNIFICANCE: Here we provide statistical and biological evidence that ribosomal protein genes exhibit important tissue-dependent variation in mRNA expression. Though these genes are most stably expressed of all investigated genes in a meta-analysis they cannot be considered true reference genes.
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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.