ArticleBMC systems biology2014
Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer.
Article in BMC systems biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Longitudinal pharmacogenomic analysis of refractory lung cancer to identify therapeutic candidates for epidermal growth factor receptor-tyrosine kinase inhibitor resistance subclones.Experimental & molecular medicine · 2025Article
- Architects and Partners: The Dual Roles of Non-coding RNAs in Gene Fusion Events.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Article
- Review
- Patient-derived cell-based pharmacogenomic assessment to unveil underlying resistance mechanisms and novel therapeutics for advanced lung cancer.Journal of experimental & clinical cancer research : CR · 2023Article
- RNA-seq data science: From raw data to effective interpretation.Frontiers in genetics · 2023Review
- In silico validation of RNA-Seq results can identify gene fusions with oncogenic potential in glioblastoma.Scientific reports · 2022Article
- Detection of gene mutations and gene-gene fusions in circulating cell-free DNA of glioblastoma patients: an avenue for clinically relevant diagnostic analysis.Molecular oncology · 2022Article
- Article
- annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions.BMC bioinformatics · 2020Article
- Human transcription factor and protein kinase gene fusions in human cancer.Scientific reports · 2020Article
- FGviewer: an online visualization tool for functional features of human fusion genes.Nucleic acids research · 2020Article
- DEEPrior: a deep learning tool for the prioritization of gene fusions.Bioinformatics (Oxford, England) · 2020Article
- Genomics of Peripheral T-Cell Lymphoma and Its Implications for Personalized Medicine.Frontiers in oncology · 2020Review
- Novel and Rare Fusion Transcripts Involving Transcription Factors and Tumor Suppressor Genes in Acute Myeloid Leukemia.Cancers · 2019Article
- Newly identified LMO3-BORCS5 fusion oncogene in Ewing sarcoma at relapse is a driver of tumor progression.Oncogene · 2019Article
- Article
- Integrative molecular profiling identifies a novel cluster of estrogen receptor-positive breast cancer in very young women.Cancer science · 2019Article
- Molecular Signatures of Fusion Proteins in Cancer.ACS pharmacology & translational science · 2019Article
- A Deep Learning Approach to the Screening of Oncogenic Gene Fusions in Humans.International journal of molecular sciences · 2019Article
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Authors and funding
10 authors.
Funding
Abstract
backgroundThe extraordinary success of imatinib in the treatment of BCR-ABL1 associated cancers underscores the need to identify novel functional gene fusions in cancer. RNA sequencing offers a genome-wide view of expressed transcripts, uncovering biologically functional gene fusions. Although several bioinformatics tools are already available for the detection of putative fusion transcripts, candidate event lists are plagued with non-functional read-through events, reverse transcriptase template switching events, incorrect mapping, and other systematic errors. Such lists lack any indication of oncogenic relevance, and they are too large for exhaustive experimental validation.
resultsWe have designed and implemented a pipeline, Pegasus, for the annotation and prediction of biologically functional gene fusion candidates. Pegasus provides a common interface for various gene fusion detection tools, reconstruction of novel fusion proteins, reading-frame-aware annotation of preserved/lost functional domains, and data-driven classification of oncogenic potential. Pegasus dramatically streamlines the search for oncogenic gene fusions, bridging the gap between raw RNA-Seq data and a final, tractable list of candidates for experimental validation.
conclusionWe show the effectiveness of Pegasus in predicting new driver fusions in 176 RNA-Seq samples of glioblastoma multiforme (GBM) and 23 cases of anaplastic large cell lymphoma (ALCL).
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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.