ArticleNucleic acids research2020
Stable gene expression for normalisation and single-sample scoring.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed.
- Trial
- Senescence-directed nanotherapy ameliorates fibrosis and overcomes immune exclusion in cancer.Science (New York, N.Y.) · 2026Article
- ATR inhibition induces NF-κB-dependent immunogenicity in Merkel cell carcinoma independent of cGAS-STING.NPJ precision oncology · 2026Article
- Tumor-Derived LAMB3 Drives Immunosuppressive LRRC15Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Deciphering the Leading-Edge Spatiotemporal Microenvironment of Hepatocellular Carcinoma for Targeted Drug Discovery Using SpaPred.International journal of molecular sciences · 2026Article
- Spatial transcriptomic atlas of aggressive osteosarcomas reveals shared immune landscape and targetable surface markers.Nature communications · 2026Article
- A metabolic constraint in de novo NAD+ synthesis drives mucosal inflammation in IBD.Journal of Crohn's & colitis · 2026Article
- Article
- Multi-Scale Mapping of Gene Expression from Whole-slide Images for Identifying Phenotype-Associated Subpopulations.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- GCNPath: introspecting drug response prediction with pathway-guided graph convolution networks.Communications biology · 2026Article
- PPAR-γ suppresses macrophage senescence and allergic airway inflammation through controlling lipid metabolic pathways.EBioMedicine · 2026Article
- Enhancing cancer killing and natural killer cell persistence by targeting NOXA, a predictor of poor patient survival.Molecular therapy. Oncology · 2026Article
- Associations of Normalization and Regularization with Machine Learning Overfitting in Cross-dataset Classification of Deaths Using Transcriptomic and Clinical Data: A Secondary Analysis of Publicly Available Databases.Journal of clinical and translational pathology · 2026Article
- Spatiotemporal transcriptomic profiling reveals upregulation of glycolysis pathway genes before overt tauopathy in the PS19 mouse model.Experimental & molecular medicine · 2026Article
- Lymphotoxin-driven cancer cell eradication by tumoricidal CD8bioRxiv : the preprint server for biology · 2025Article
- Pan-cancer analysis reveals context-dependent roles of LINE-1 ORF1p in immune regulation and copy number alterations.bioRxiv : the preprint server for biology · 2025Article
- EWS::FLI1 expression in human embryonic mesenchymal stem cells leads to transcriptional reprograming, defective DNA damage repair and Ewing sarcoma.Nature communications · 2025Article
- Spatial transcriptomics exploration of the primary neuroblastoma microenvironment in archived FFPE samples unveils novel paracrine interactions.The Journal of pathology · 2025Article
- Divergent cytokine and transcriptional signatures control functional T follicular helper cell heterogeneity.Nature immunology · 2025Article
- Selecting Optimal Housekeeping Genes for RT-qPCR in Endometrial Cancer Studies: A Narrative Review.International journal of molecular sciences · 2025Review
5 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene expression signatures have been critical in defining the molecular phenotypes of cells, tissues, and patient samples. Their most notable and widespread clinical application is stratification of breast cancer patients into molecular (PAM50) subtypes. The cost and relatively large amounts of fresh starting material required for whole-transcriptome sequencing has limited clinical application of thousands of existing gene signatures captured in repositories such as the Molecular Signature Database. We identified genes with stable expression across a range of abundances, and with a preserved relative ordering across thousands of samples, allowing signature scoring and supporting general data normalisation for transcriptomic data. Our new method, stingscore, quantifies and summarises relative expression levels of signature genes from individual samples through the inclusion of these 'stably-expressed genes'. We show that our list of stable genes has better stability across cancer and normal tissue data than previously proposed gene sets. Additionally, we show that signature scores computed from targeted transcript measurements using stingscore can predict docetaxel response in breast cancer patients. This new approach to gene expression signature analysis will facilitate the development of panel-type tests for gene expression signatures, thus supporting clinical translation of the powerful insights gained from cancer transcriptomic studies.
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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.