Chromosome translocation and gene fusion are frequent events in the human genome and are often the cause of many types of tumor.
ChimerDB is designed to be a knowledgebase of fusion transcripts collected from various public resources such as the Sanger CGP, OMIM, PubMed, and Mitelman’s database.
There have been significant progresses in detecting chimeric transcripts during last few years. Novel fusion transcripts were identified in major solid tumors of organs such as prostate, lung, and breast, and the discovery is being accelerated with the introduction of next-generation sequencing technologies. It is certain that the impact of discovering fusion genes will grow exponentially on cancer research in the coming decades, and the up-to-date knowledgebase is of great value for the scientific community. Here, we present the updated version of the ChimerDB, whose import features are listed as below.
Important Features in the update version
- More sensitive detection of chimeric transcripts by careful analysis of genomics alignments (coverage, break point, gene structure, etc)
- Introduction of confidence classes A, B, C, taking the gene structure into consideration
- Identification of intra-chromosomal fusion transcripts due to deletion of large chromosomal segment
- Analysis of short read sequences in the NCBI’s SRA (short read archive) database
- Data coverage
- Significant increase in the number of transcript sequences in the GenBank
- 454 and Solexa transcript sequences in the SRA database
- Update of Sanger CGP, OMIM, Mitelman’s database
- Extensive collection of fusion genes in the recent publications
- User interface
- Support for diverse and detailed searches (gene, gene pair, chromosomal band, fusion transcript, and tissue)
- Dedicated alignment viewer
- Informative presentation style for PubMed articles
- Enhanced output GUI and removal of redundant information