ArticleBMC bioinformatics2014
Ensemble analyses improve signatures of tumour hypoxia and reveal inter-platform differences.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Review
- Harnessing transcriptional regulation of alternative end-joining to predict cancer treatment.NAR cancer · 2025Article
- Defining hypoxia in cancer: A landmark evaluation of hypoxia gene expression signatures.Cell genomics · 2025Article
- Identification of Hypoxia-ALCAMAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Multi-omics characterization of autophagy-related molecular features for therapeutic targeting of autophagy.Nature communications · 2022Article
- A Novel hepatocellular carcinoma specific hypoxic related signature for predicting prognosis and therapeutic responses.Frontiers in immunology · 2022Article
- Hypoxia and its impact on the tumour microenvironment of gastroesophageal cancers.World journal of gastrointestinal oncology · 2021Review
- Derivation and Application of Molecular Signatures to Prostate Cancer: Opportunities and Challenges.Cancers · 2021Review
- Hypoxia and the phenomenon of immune exclusion.Journal of translational medicine · 2021Review
- Hypoxia Contributes to Poor Prognosis in Primary IDH-wt GBM by Inducing Tumor Cells MES-Like Transformation Trend and Inhibiting Immune Cells Activity.Frontiers in oncology · 2021Article
- A Hypoxia-Associated Prognostic Gene Signature Risk Model and Prognosis Predictors in Gliomas.Frontiers in oncology · 2021Article
- Tumor Hypoxia Regulates Immune Escape/Invasion: Influence on Angiogenesis and Potential Impact of Hypoxic Biomarkers on Cancer Therapies.Frontiers in immunology · 2020Review
- Modelling of hypoxia gene expression for three different cancer cell lines.International journal of computational biology and drug design · 2020Article
- Predictive value of hypoxia, metabolism and immune factors for prognosis in hepatocellular carcinoma: a retrospective analysis and multicenter validation study.Journal of Cancer · 2020Article
- Hypoxia-Associated Prognostic Markers and Competing Endogenous RNA Co-Expression Networks in Breast Cancer.Frontiers in oncology · 2020Article
- Guidelines for using sigQC for systematic evaluation of gene signatures.Nature protocols · 2019Article
- Characterization of Hypoxia-associated Molecular Features to Aid Hypoxia-Targeted Therapy.Nature metabolism · 2019Article
- Prediction of early breast cancer patient survival using ensembles of hypoxia signatures.PloS one · 2018Article
- In vitro downregulated hypoxia transcriptome is associated with poor prognosis in breast cancer.Molecular cancer · 2017Article
- Genomic alterations underlie a pan-cancer metabolic shift associated with tumour hypoxia.Genome biology · 2016Article
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5 authors.
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Abstract
backgroundThe reproducibility of transcriptomic biomarkers across datasets remains poor, limiting clinical application. We and others have suggested that this is in-part caused by differential error-structure between datasets, and their incomplete removal by pre-processing algorithms.
methodsTo test this hypothesis, we systematically assessed the effects of pre-processing on biomarker classification using 24 different pre-processing methods and 15 distinct signatures of tumour hypoxia in 10 datasets (2,143 patients).
resultsWe confirm strong pre-processing effects for all datasets and signatures, and find that these differ between microarray versions. Importantly, exploiting different pre-processing techniques in an ensemble technique improved classification for a majority of signatures.
conclusionsAssessing biomarkers using an ensemble of pre-processing techniques shows clear value across multiple diseases, datasets and biomarkers. Importantly, ensemble classification improves biomarkers with initially good results but does not result in spuriously improved performance for poor biomarkers. While further research is required, this approach has the potential to become a standard for transcriptomic biomarkers.
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