ArticleScientific reports2015
Large-scale RNA-Seq Transcriptome Analysis of 4043 Cancers and 548 Normal Tissue Controls across 12 TCGA Cancer Types.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers, 3 of them syntheses that pooled it.
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Who cites it
69 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Artificial intelligence-based non-small cell lung cancer transcriptome RNA-sequence analysis technology selection guide.Frontiers in bioengineering and biotechnology · 2023Pooled it
- Clinical significance of miRNA‑1 and its potential target gene network in lung squamous cell carcinoma.Molecular medicine reports · 2019Pooled it
- Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer.Molecular autism · 2019Pooled it
- On why cancer cells require a great amount of glucose.Quantitative biology (Beijing, China) · 2026Article
- Recapitulating patient-to-patient colorectal cancer tumor heterogeneity using patient-derived xenograft cells in an engineered tissue model.Acta biomaterialia · 2026Article
- Extending differential gene expression testing to handle genome aneuploidy in cancer.PLoS computational biology · 2026Article
- Artemis: Harnessing Knowledge Graphs for Next-Generation Drug Target Prioritization.Computational and structural biotechnology journal · 2026Article
- Recapitulating Patient-to-Patient Colorectal Cancer Tumor Heterogeneity Using Patient-Derived Xenograft Cells in an Engineered Tissue Model.bioRxiv : the preprint server for biology · 2025Article
- Diet therapy abates mutant APC and KRas effects by reshaping plasma membrane cholesterol nanodomains.Biophysical journal · 2025Article
- Population-level allelic dispersion modeling by maelstRom yields genome-wide maps of allele-specific dysregulation during early carcinogenesis.GigaScience · 2025Article
- Role of MLIP in burn-induced sepsis and insights into sepsis-associated cancer progression.Frontiers in immunology · 2025Article
- Molecular Subtypes of High-Grade Serous Ovarian Cancer across Racial Groups and Gene Expression Platforms.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2024Article
- Clover: An unbiased method for prioritizing differentially expressed genes using a data-driven approach.Genes to cells : devoted to molecular & cellular mechanisms · 2024Article
- Article
- Sparassis latifolia and exercise training as complementary medicine mitigated the 5-fluorouracil potent side effects in mice with colorectal cancer: bioinformatics approaches, novel monitoring pathological metrics, screening signatures, and innovative management tactic.Cancer cell international · 2024Article
- A deep learning method for classification of HNSCC and HPV patients using single-cell transcriptomics.Frontiers in molecular biosciences · 2024Article
- Molecular subtypes of high-grade serous ovarian cancer across racial groups and gene expression platforms.bioRxiv : the preprint server for biology · 2023Article
- Developments and challenges in neoadjuvant therapy for locally advanced pancreatic cancer.World journal of gastroenterology · 2023Review
- Candidate pathway analysis of surfactant proteins identifies CTSH and SFTA2 that influences lung cancer risk.Human molecular genetics · 2023Article
- Mutant APC reshapes Wnt signaling plasma membrane nanodomains by altering cholesterol levels via oncogenic β-catenin.Nature communications · 2023Article
9 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Cancer Genome Atlas (TCGA) has accrued RNA-Seq-based transcriptome data for more than 4000 cancer tissue samples across 12 cancer types, translating these data into biological insights remains a major challenge. We analyzed and compared the transcriptomes of 4043 cancer and 548 normal tissue samples from 21 TCGA cancer types, and created a comprehensive catalog of gene expression alterations for each cancer type. By clustering genes into co-regulated gene sets, we identified seven cross-cancer gene signatures altered across a diverse panel of primary human cancer samples. A 14-gene signature extracted from these seven cross-cancer gene signatures precisely differentiated between cancerous and normal samples, the predictive accuracy of leave-one-out cross-validation (LOOCV) were 92.04%, 96.23%, 91.76%, 90.05%, 88.17%, 94.29%, and 99.10% for BLCA, BRCA, COAD, HNSC, LIHC, LUAD, and LUSC, respectively. A lung cancer-specific gene signature, containing SFTPA1 and SFTPA2 genes, accurately distinguished lung cancer from other cancer samples, the predictive accuracy of LOOCV for TCGA and GSE5364 data were 95.68% and 100%, respectively. These gene signatures provide rich insights into the transcriptional programs that trigger tumorigenesis and metastasis, and many genes in the signature gene panels may be of significant value to the diagnosis and treatment of cancer.
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