ChimerDB--a knowledgebase for fusion sequences - PubMed (original) (raw)

ChimerDB--a knowledgebase for fusion sequences

Namshin Kim et al. Nucleic Acids Res. 2006.

Abstract

Chromosome translocation and gene fusion are frequent events in the human genome and are often the cause of many types of tumor. ChimerDB is the database of fusion sequences encompassing bioinformatics analysis of mRNA and expressed sequence tag (EST) sequences in the GenBank, manual collection of literature data and integration with other known database such as OMIM. Our bioinformatics analysis identifies the fusion transcripts that have non-overlapping alignments at multiple genomic loci. Fusion events at exon-exon borders are selected to filter out the cloning artifacts in cDNA library preparation. The result is classified into two groups--genuine chromosome translocation and fusion between neighboring genes owing to intergenic splicing. We also integrated manually collected literature and OMIM data for chromosome translocation as an aid to assess the validity of each fusion event. The database is available at http://genome.ewha.ac.kr/ChimerDB/ for human, mouse and rat genomes.

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Figures

Figure 1

(A) Part of the output page from ChimerDB. (B) Custom genome browser for RUNX1T1 genomic locus to visualize fusion transcripts. Red dot indicates the fusion point.

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