Table 4.
Databases of gene fusions.
| Database name and URL | Description | Database size | Source of data | Reference |
|---|---|---|---|---|
| Mitelman https://mitelmandatabase.isb-cgc.org | Relates gene fusions and other chromosomal aberrations to tumor characteristics, based either on individual cases or associations | Total number of unique gene fusions 32,962, Total number of genes involved 14,016 as for April 2022 | Manual curation of literature | Denomy et al.255 |
| COSMIC: the Catalogue Of Somatic Mutations In Cancer https://cancer.sanger.ac.uk | Catalog of translocations and fusions between gene pairs supplemented with extensive clinical data | 19 368 Gene Fusions as for August 2018 | Manual curation of literature | Tate et al.,262 |
| TumorFusions: TCGA Fusion Gene Data portal https://tumorfusions.org/ | An integrative resource for cancer-associated transcript fusions giving a landscape of cancer-associated fusions using the pipeline for RNA sequencing data analysis | Total fusion called across multiple cancer types is 20731 as of July 2017 | Integrated analysis of RNA-seq and DNA-seq data from TCGA | Hu et al.,263 Yoshihara et al.264 |
| ChimerDB http://www.kobic.re.kr/chimerdb/ | Fusion transcripts across multiple species knowledgebase and information on cancer breakpoints | 67 610 fusion gene pairs, of which 1597 fusion genes with publication support as for November 2019 | Sequencing data from TCGA and PubMed publications curation | Jang et al.265 |
| ChiTaRS http://chitars.md.biu.ac.il/ | Catalogue of fusion transcripts in humans, mice, fruit flies, zebrafishes, cows, rats, pig and yeast using RNA-seq data | 111,582 fusion transcripts in humans, mice, fruit flies, rats, zebrafishes, cows, pigs, and yeast as for 2019 | EST and mRNA sequences analysis from NCBI/GenBank and review of publications by Mertens et al. and from the Mitelman collection | Balamurali et al.266 |
| FusionCancer http://donglab.ecnu.edu.cn/databases/FusionCancer/ | Fusion gene database derived exclusively from cancer RNA-seq data | 11 839 gene fusions as for 2015 | Analysis of 591 RNA-seq cancer datasets | Wang et al.267 |
| FARE-CAFÉ http://ppi.bioinfo.asia.edu.tw/FARE-CAFE | Database of functional and regulatory elements in gene fusion events related to cancer | 1587 gene fusions as for 2015 | Combination of information from different sources, including TICdb, dbCRID, NCBI, and miRTarBase | Korla et al.268 |
| HYBRIDdb http://www.primate.or.kr/hybriddb | Database of hybrid genes in the human genome | 3404 gene fusions as for 2007 | Data from INSDC about mRNA, EST, cDNA, and genomic DNA sequences | Kim et al.269 |
| FusionGDB 2.0 https://compbio.uth.edu/FusionGDB2/ | Fusion Gene annotation DataBase | 102 645 fusion genes with 16 146 in-frame as for 2021 | Combined data from ChiTaRS 5.0 and ChimerDB 4.0 and manual curation of PubMed articles for the most frequent fusions | Kim et al.270 |
| dbCRID http://dbCRID.biolead.org | Curated database of human chromosomal rearrangements, associated diseases and clinical symptoms | 2643 chromosome rearrangements as for 2010 | Manual curation of literature | Kong et al.271 |
| TICdb http://www.unav.es/genetica/TICdb/ | Finely mapped translocation breakpoints in cancer | 1374 fusion sequences from 431 different genes as for 2007 | Databases analysis and publications review | Novo et al.272 |
| KuNG FU (KiNase Gene FUsion) http://www.kungfudb.org/ | Database containing in-frame kinase gene fusions with intact kinase domain in cell lines | 108 total fusions as for January 2021 | Manual curation of literature | Kim et al.269 |
EST, expressed sequence tag; FISH, fluorescent in situ hybridization; TCGS, The Cancer Genome Atlas.