ArticleNucleic acids research2020
ChimerDB 4.0: an updated and expanded database of fusion genes.
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 71 papers.
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Who cites it
71 citing papers in PubMed.
- Phase II trial of imatinib mesylate in patients with PDGFRA/B-negative hypereosinophilic syndrome.British journal of haematology · 2024Trial
- Fusion gene map of acute leukemia revealed by transcriptome sequencing of a consecutive cohort of 1000 cases in a single center.Blood cancer journal · 2021Trial
- A Practical Compass to Biological Digital Resources and Omics Integration in Ewing Sarcoma.Methods in molecular biology (Clifton, N.J.) · 2027Article
- EML4-ALK fusion rewires transcriptomic, miRNA, and CAF-associated programs in non-small cell lung cancer.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2026Article
- FuDiCo: Gene Fusion-Initiated Path Propagation for Disease Comorbidity Prediction.Current issues in molecular biology · 2026Article
- Fusion-positive rhabdomyosarcoma oncofusions share a common interactome.Nature communications · 2026Article
- Patient-derived pediatric brain tumor orthotopic xenografts and tumor organoids faithfully recapitulate primary tumors.Science advances · 2026Article
- Long-Read Transcriptome Sequencing and Functional Validation Reveals Novel and Oncogenic Gene Fusions in Fusion Panel-Negative Gliomas.bioRxiv : the preprint server for biology · 2026Article
- GFSeeker: a splicing-graph-based approach for accurate gene fusion detection from long-read RNA sequencing data.Briefings in bioinformatics · 2026Article
- Identification of aeLife · 2026Article
- ESR1 fusions in breast cancer: functions, mechanisms and therapeutic opportunities.Translational breast cancer research : a journal focusing on translational research in breast cancer · 2026Review
- Mass Spectrometry-Based Validation of Chimeric RNAs.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Detection of Chimeric RNAs from RNA-Seq Data with ChiTaRS 8.0: Insights for Liquid Biopsy and Drug Target Identification.Methods in molecular biology (Clifton, N.J.) · 2026Article
- RoCK and ROI: single-cell transcriptomics with multiplexed enrichment of selected transcripts and region-specific sequencing.Nature communications · 2025Article
- Fusion transcripts landscape in hepatocellular carcinoma and potential impact on the expression of fusion partners.RNA biology · 2025Article
- Regulatory Mechanisms and Functional Roles of Readthrough Transcripts in Tumorigenesis.International journal of molecular sciences · 2025Review
- PACLseq: A Standalone Diagnostic Method for Ph-Like Acute Lymphoblastic Leukemia Using Nanopore Sequencing.MedComm · 2025Article
- Combining panel-based and whole-transcriptome-based gene fusion detection by long-read sequencing.Cell reports methods · 2025Article
- A pan-cancer atlas of therapeutic T cell targets.bioRxiv : the preprint server for biology · 2025Article
- Uncovering the domain language of protein functionality and cell phenotypes using DANSy.bioRxiv : the preprint server for biology · 2025Article
11 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors.
Funding
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Abstract
Fusion genes represent an important class of biomarkers and therapeutic targets in cancer. ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data (ChimerSeq) and text mining of publications (ChimerPub) with extensive manual annotations (ChimerKB). In this update, we present all three modules substantially enhanced by incorporating the recent flood of deep sequencing data and related publications. ChimerSeq now covers all 10 565 patients in the TCGA project, with compilation of computational results from two reliable programs of STAR-Fusion and FusionScan with several public resources. In sum, ChimerSeq includes 65 945 fusion candidates, 21 106 of which were predicted by multiple programs (ChimerSeq-Plus). ChimerPub has been upgraded by applying a deep learning method for text mining followed by extensive manual curation, which yielded 1257 fusion genes including 777 cases with experimental supports (ChimerPub-Plus). ChimerKB includes 1597 fusion genes with publication support, experimental evidences and breakpoint information. Importantly, we implemented several new features to aid estimation of functional significance, including the fusion structure viewer with domain information, gene expression plot of fusion positive versus negative patients and a STRING network viewer. The user interface also was greatly enhanced by applying responsive web design. ChimerDB 4.0 is available at http://www.kobic.re.kr/chimerdb/.
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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.