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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
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FusionGDB: fusion gene annotation DataBase

Pora Kim1, Xiaobo Zhou1,2,3

  • 1Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

Nucleic Acids Research
|November 9, 2018
PubMed

Insights

FusionGDB is a new database that catalogs over 48,000 cancer gene fusions. This resource aids in understanding gene fusion functions and discovering new cancer biomarkers and therapies.

Area of Science:

  • Genomics and Bioinformatics
  • Cancer Research
  • Molecular Biology

Background:

  • Gene fusions, resulting from chromosomal rearrangements, are key features of cancer genomes.
  • Numerous fusion genes (FGs) serve as critical biomarkers and therapeutic targets in various cancers.
  • Understanding FG function is crucial for advancing cancer diagnostics and treatment.

Purpose of the Study:

  • To establish FusionGDB, a comprehensive database for pan-cancer gene fusion annotation.
  • To facilitate the understanding of FG functions across different cancer types.
  • To promote the discovery of novel, clinically relevant fusion genes.

Main Methods:

  • Collected approximately 48,117 FGs from three major resources: ChiTaRS 3.1, TumorFusions, and TCGA.
  • Performed functional annotations, including open reading frame (ORF) assignment and protein feature retention analysis (39 features).
  • Generated fusion transcript and amino acid sequences considering multiple breakpoints and isoforms.

Main Results:

  • Identified 331 in-frame FGs retaining kinase domains, 303 retaining DNA-binding domains, and 667 retaining epigenetic factor domains.
  • Discovered 976 FGs with lost protein-protein interaction capabilities.
  • FusionGDB offers six annotation categories: FusionGeneSummary, FusionProtFeature, FusionGeneSequence, FusionGenePPI, RelatedDrug, and RelatedDisease.

Conclusions:

  • FusionGDB provides a valuable, integrated resource for exploring cancer gene fusions.
  • The database facilitates functional annotation and characterization of FGs.
  • FusionGDB supports research into FG-driven mechanisms and potential therapeutic strategies in oncology.

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