ArticleOncogene2012
A general method to derive robust organ-specific gene expression-based differentiation indices: application to thyroid cancer diagnostic.
Article in Oncogene, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers, 3 of them syntheses that pooled it.
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Who cites it
91 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Network medicine approaches for identification of novel prognostic systems biomarkers and drug candidates for papillary thyroid carcinoma.Journal of cellular and molecular medicine · 2023Pooled it
- Adding pieces to the puzzle of differentiated-to-anaplastic thyroid cancer evolution: the oncogene E2F7.Cell death & disease · 2023Pooled it
- Deciphering radiological stable disease to immune checkpoint inhibitors.Annals of oncology : official journal of the European Society for Medical Oncology · 2022Pooled it
- Analysis and validation of prognostic markers for thyroid cancer by single-cell and bulk RNA sequencing.Translational cancer research · 2026Article
- Spatial and single-nuclei transcriptomics reveals idiosyncratic and generic patterns in papillary and anaplastic thyroid cancers.Molecular oncology · 2026Article
- Role of the ETV5/p38 Signaling Axis in Aggressive Thyroid Cancer Cells.Molecular cancer therapeutics · 2026Article
- Multiomics Profiling Reveals Distinct Immunosuppression and Metabolic Dysregulation in Aggressive Subtypes of Thyroid Cancer.Molecular & cellular proteomics : MCP · 2026Article
- Disulfiram metabolite Cu(DDC)EBioMedicine · 2026Article
- DNMT2 inhibits anaplastic thyroid cancer progression by downregulating 5'tiRNACell death & disease · 2026Article
- Two Cohorts, One Network: Consensus Master Regulators Orchestrating Papillary Thyroid Carcinoma.International journal of molecular sciences · 2025Article
- CRABP1 Signalosomes in Non-Canonical Actions of Retinoic Acid-Maintaining Health and Preventing Thyroid Dysfunction in Aging.Endocrines · 2025Article
- Identification of thyroid cancer biomarkers using WGCNA and machine learning.European journal of medical research · 2025Article
- Multi-omics clustering analysis carries out the molecular-specific subtypes of thyroid carcinoma: implicating for the precise treatment strategies.Genes and immunity · 2025Article
- Identifying CSNK1E as a therapeutic target in thyroid cancer among the core circadian clock genes.Histochemistry and cell biology · 2025Article
- Targeting CDK2 Confers Vulnerability to Lenvatinib Via Driving Senescence in Anaplastic Thyroid Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Article
- Fatty acid metabolism influences the immune microenvironment in papillary thyroid cancer and identifies SCD as a novel biomarker.Frontiers in endocrinology · 2025Article
- Article
- Identification of GPX3 and JUN as Tumor Suppressors in Thyroid Cancer through Integrated WGCNA and Mendelian Randomization.Journal of Cancer · 2025Article
- A Six-Gene Mitochondrial Signature Predicts Prognosis in Dedifferentiated Thyroid Cancer.International journal of general medicine · 2025Article
31 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Differentiation is central to development, while dedifferentiation is central to cancer progression. Hence, a quantitative assessment of differentiation would be most useful. We propose an unbiased method to derive organ-specific differentiation indices from gene expression data and demonstrate its usefulness in thyroid cancer diagnosis. We derived a list of thyroid-specific genes by selecting automatically those genes that are expressed at higher level in the thyroid than in any other organ in a normal tissue's genome-wide gene expression compendium. The thyroid index of a tissue was defined as the median expression of these thyroid-specific genes in that tissue. As expected, the thyroid index was inversely correlated with meta-PCNA, a proliferation metagene, across a wide range of thyroid tumors. By contrast, the two indices were positively correlated in a time course of thyroid-stimulating hormone (TSH) activation of primary thyrocytes. Thus, the thyroid index captures biological information not integrated by proliferation rates. The differential diagnostic of follicular thyroid adenomas and follicular thyroid carcinoma is a notorious challenge for pathologists. The thyroid index discriminated them as accurately as did machine-learning classifiers trained on the genome-wide cancer data. Hence, although it was established exclusively from normal tissue data, the thyroid index integrates the relevant diagnostic information contained in tumoral transcriptomes. Similar results were obtained for the classification of the follicular vs classical variants of papillary thyroid cancers, that is, tumors dedifferentiating along a different route. The automated procedures demonstrated in the thyroid are applicable to other organs.
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