ArticleNucleic acids research2017
ChiPPI: a novel method for mapping chimeric protein-protein interactions uncovers selection principles of protein fusion events in cancer.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.
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Who cites it
20 citing papers in PubMed, 1 synthesis or guideline pooled it, 36 citations in OpenAlex.
- Interactomics in plant defence: progress and opportunities.Molecular biology reports · 2023Pooled it
- Fusion oncoproteins orchestrate tumorigenesis and sustain malignant progression via a positive feedback mechanism.Cell & bioscience · 2026Review
- 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
- Apatinib Degrades PD-L1 and Reconstitutes Colon Cancer Microenvironment via the Regulation of Myoferlin.Cancers · 2025Article
- FusionPDB: a knowledgebase of human fusion proteins.Nucleic acids research · 2024Article
- The Landscape of Expressed Chimeric Transcripts in the Blood of Severe COVID-19 Infected Patients.Viruses · 2023Article
- 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
- EvoProDom: evolutionary modeling of protein families by assessing translocations of protein domains.FEBS open bio · 2021Article
- Emerging Role of Chimeric RNAs in Cell Plasticity and Adaptive Evolution of Cancer Cells.Cancers · 2021Review
- Pathway perturbations in signaling networks: Linking genotype to phenotype.Seminars in cell & developmental biology · 2020Review
- The landscape of chimeric RNAs in non-diseased tissues and cells.Nucleic acids research · 2020Article
- ChiTaRS 5.0: the comprehensive database of chimeric transcripts matched with druggable fusions and 3D chromatin maps.Nucleic acids research · 2020Article
- ProtFus: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins.PLoS computational biology · 2019Article
- The chromatin remodeler Chd1 regulates cohesin in budding yeast and humans.Scientific reports · 2019Article
- Building Bridges Between Structural and Network-Based Systems Biology.Molecular biotechnology · 2019Review
- FusionGDB: fusion gene annotation DataBase.Nucleic acids research · 2019Article
- Synstable Fusion: A Network-Based Algorithm for Estimating Driver Genes in Fusion Structures.Molecules (Basel, Switzerland) · 2018Article
- FusionPathway: Prediction of pathways and therapeutic targets associated with gene fusions in cancer.PLoS computational biology · 2018Article
- A Novel Approach for Identifying Relevant Genes for Breast Cancer Survivability on Specific Therapies.Evolutionary bioinformatics online · 2018Review
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Fusion proteins, comprising peptides deriving from the translation of two parental genes, are produced in cancer by chromosomal aberrations. The expressed fusion protein incorporates domains of both parental proteins. Using a methodology that treats discrete protein domains as binding sites for specific domains of interacting proteins, we have cataloged the protein interaction networks for 11 528 cancer fusions (ChiTaRS-3.1). Here, we present our novel method, chimeric protein-protein interactions (ChiPPI) that uses the domain-domain co-occurrence scores in order to identify preserved interactors of chimeric proteins. Mapping the influence of fusion proteins on cell metabolism and pathways reveals that ChiPPI networks often lose tumor suppressor proteins and gain oncoproteins. Furthermore, fusions often induce novel connections between non-interactors skewing interaction networks and signaling pathways. We compared fusion protein PPI networks in leukemia/lymphoma, sarcoma and solid tumors finding distinct enrichment patterns for each disease type. While certain pathways are enriched in all three diseases (Wnt, Notch and TGF β), there are distinct patterns for leukemia (EGFR signaling, DNA replication and CCKR signaling), for sarcoma (p53 pathway and CCKR signaling) and solid tumors (FGFR and EGFR signaling). Thus, the ChiPPI method represents a comprehensive tool for studying the anomaly of skewed cellular networks produced by fusion proteins in cancer.
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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.