ArticleCommunications biology2024
Pan-cancer discovery of somatic mutations from RNA sequencing data.
Article in Communications biology, 2024. 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.
- Validation of next‑generation sequencing‑derived circulating mRNA variants as potential diagnostic tools in hepatocellular carcinoma and cholangiocarcinoma.Oncology reports · 2026Article
- Somatic mosaicism in the brain: linking development, ageing and neurodegeneration.Nature reviews. Neurology · 2026Review
- Rab5 nucleotide binding promotes oxidative metabolism to fuel hepatocellular carcinoma cell proliferation.The Journal of biological chemistry · 2026Article
- The actionable transcriptome: a framework for incorporating RNA sequencing into precision oncology.Nature reviews. Clinical oncology · 2026Review
- Dual-biomarkers encoding tumor-activatable minicircles with scaffold/matrix attachment region motif for sensitive and sustained blood and urine-based cancer detection.Cancer cell international · 2026Article
- Small Nucleotide Variant Analysis Using RNA Fusion Panel (SMURF): Making the Most of RNAseq Data in Solid Tumours.Journal of clinical laboratory analysis · 2026Article
- Article
- Transient receptor potential canonical 3 is required for HPV-induced malignant transformation of cervical epithelial cells.Communications biology · 2026Article
- OncoDB 2.0: a comprehensive platform for integrated pan-cancer omics analysis.Nucleic acids research · 2026Article
- Ficoll-based isolation biases the profiling of immune cells and leukemic blasts in AML samples.Frontiers in immunology · 2026Article
- Prognostic significance of the MELK/TMPO-AS1/hsa-let-7b-5p network in lung adenocarcinoma.Frontiers in oncology · 2026Article
- TGF-β Receptor Inhibitor SB431542 Enhanced the Sensitivity of Gastric Cancer to 5-Fluorouracil: New Combined Targeted Therapy.International journal of molecular sciences · 2025Article
- Long noncoding RNA TMPO-AS1 upregulates chromosomal passenger complex expression to promote cell proliferation in lung cancer via sponging microRNA let-7b-5p.Cell division · 2025Article
- Comprehensive molecular characterization of craniopharyngiomas using whole transcriptome and spatial transcriptomics approaches.Brain tumor pathology · 2025Article
- Single-cell multi-omics in cancer immunotherapy: from tumor heterogeneity to personalized precision treatment.Molecular cancer · 2025Review
- Genomic Insights into Tumorigenesis in Newly Diagnosed Multiple Myeloma.Diagnostics (Basel, Switzerland) · 2025Article
- Interaction between NF-κB and PLAC8 impairs autophagy providing a survival advantage to prostate cells transformed by cadmium.Science advances · 2025Article
- hsa-let-7b-5p/TMPO-AS1-mediated ceRNA networks are linked to poor prognosis for lung cancer patients with FOXM1/MAD2L1 axis.Discover oncology · 2025Article
- Inorganic Arsenic Induces Elevated p53 Levels with Altered Functionality Impacting the Expression of Toll-like Receptor 3 and Other Target Genes in Immortalized Prostate Epithelial Cells.International journal of molecular sciences · 2025Article
- Etoposide-induced protein 2.4 homolog promotes argininosuccinate synthase 1 and cancer cell survival upon arginine deprivation.Cellular & molecular biology letters · 2025Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Identification of somatic mutations (SMs) is essential for characterizing cancer genomes. While DNA-seq is the prevalent method for identifying SMs, RNA-seq provides an alternative strategy to discover tumor mutations in the transcribed genome. Here, we have developed a machine learning based pipeline to discover SMs based on RNA-seq data (designated as RNA-SMs). Subsequently, we have conducted a pan-cancer analysis to systematically identify RNA-SMs from over 8,000 tumors in The Cancer Genome Atlas (TCGA). In this way, we have identified over 105,000 novel SMs that had not been reported in previous TCGA studies. These novel SMs have significant clinical implications in designing targeted therapy for improved patient outcomes. Further, we have combined the SMs identified by both RNA-seq and DNA-seq analyses to depict an updated mutational landscape across 32 cancer types. This new online SM atlas, OncoDB ( https://oncodb.org ), offers a more complete view of gene mutations that underline the development and progression of various cancers.
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