ArticleNature biotechnology2009
An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer.
Article in Nature biotechnology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers, 1 of them a synthesis that pooled it.
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Who cites it
48 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Transcriptome meta-analysis of lung cancer reveals recurrent aberrations in NRG1 and Hippo pathway genes.Nature communications · 2014Pooled it
- Detection, Characterization, and Inhibition of FGFR-TACC Fusions in IDH Wild-type Glioma.Clinical cancer research : an official journal of the American Association for Cancer Research · 2015Trial
- PYCR1 induces ferroptosis via the PI3K/Akt signaling pathway to regulate the proliferation and migration of osteosarcoma.Translational oncology · 2026Article
- ESR1 fusion proteins in breast cancer: distinguishing oncogenic drivers from passenger events.Oncogene · 2026Review
- Genomic and immunogenomic analysis of three prognostic signature genes in LUAD.BMC bioinformatics · 2023Article
- Pathogenesis and prognosis of primary oral squamous cell carcinoma based on microRNAs target genes: a systems biology approach.Genomics & informatics · 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
- Therapeutic Targeting of Nemo-like Kinase in Primary and Acquired Endocrine-resistant Breast Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2021Article
- A Novel Neoplastic Fusion Transcript,Clinical cancer research : an official journal of the American Association for Cancer Research · 2021Article
- Hsa-miR-21-3p associates with breast cancer patient survival and targets genes in tumor suppressive pathways.PloS one · 2021Article
- Universal concept signature analysis: genome-wide quantification of new biological and pathological functions of genes and pathways.Briefings in bioinformatics · 2020Article
- Landscape analysis of adjacent gene rearrangements reveals BCL2L14-ETV6 gene fusions in more aggressive triple-negative breast cancer.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Article
- Molecular Signatures of Fusion Proteins in Cancer.ACS pharmacology & translational science · 2019Article
- Identification of Prognostic Dosage-Sensitive Genes in Colorectal Cancer Based on Multi-Omics.Frontiers in genetics · 2019Article
- Synstable Fusion: A Network-Based Algorithm for Estimating Driver Genes in Fusion Structures.Molecules (Basel, Switzerland) · 2018Article
- ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues.Genome biology · 2018Article
- ChiPPI: a novel method for mapping chimeric protein-protein interactions uncovers selection principles of protein fusion events in cancer.Nucleic acids research · 2017Article
- pETM: a penalized Exponential Tilt Model for analysis of correlated high-dimensional DNA methylation data.Bioinformatics (Oxford, England) · 2017Article
- Identification of MYST3 as a novel epigenetic activator of ERα frequently amplified in breast cancer.Oncogene · 2017Article
Corrections and comments
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Authors and funding
16 authors.
Funding
Abstract
Cancer genomes contain many aberrant gene fusions-a few that drive disease and many more that are nonspecific passengers. We developed an algorithm (the concept signature or 'ConSig' score) that nominates biologically important fusions from high-throughput data by assessing their association with 'molecular concepts' characteristic of cancer genes, including molecular interactions, pathways and functional annotations. Copy number data supported candidate fusions and suggested a breakpoint principle for intragenic copy number aberrations in fusion partners. By analyzing lung cancer transcriptome sequencing and genomic data, we identified a novel R3HDM2-NFE2 fusion in the H1792 cell line. Lung tissue microarrays revealed 2 of 76 lung cancer patients with genomic rearrangement at the NFE2 locus, suggesting recurrence. Knockdown of NFE2 decreased proliferation and invasion of H1792 cells. Together, these results present a systematic analysis of gene fusions in cancer and describe key characteristics that assist in new fusion discovery.
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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.