FARE-CAFE: a database of functional and regulatory elements of cancer-associated fusion events

Abstract

Chromosomal translocation (CT) is of enormous clinical interest because this disorder is associated with various major solid tumors and leukemia. A tumor-specific fusion gene event may occur when a translocation joins two separate genes. Currently, various CT databases provide information about fusion genes and their genomic elements. However, no database of the roles of fusion genes, in terms of essential functional and regulatory elements in oncogenesis, is available. FARE-CAFE is a unique combination of CTs, fusion proteins, protein domains, domain–domain interactions, protein–protein interactions, transcription factors and microRNAs, with subsequent experimental information, which cannot be found in any other CT database. Genomic DNA information including, for example, manually collected exact locations of the first and second break points, sequences and karyotypes of fusion genes are included. FARE-CAFE will substantially facilitate the cancer biologist’s mission of elucidating the pathogenesis of various types of cancer. This database will ultimately help to develop ‘novel’ therapeutic approaches.Database URL: http://ppi.bioinfo.asia.edu.tw/FARE-CAFE

Discovering and understanding oncogenic gene fusions through data intensive computational approaches

“…A study of intrinsic disorder in fusion proteins found that translocated proteins are more intrinsically disordered and tend to have fewer Pfam domains than non-translocated proteins ( 87 ) (Figure 3B ), which has recently been demonstrated again ( 88 ). However, another survey of fusion proteins showed that they contain complete protein domains much more frequently than would be expected if fusion transcripts were generated from randomly fused protein coding sequences ( 89 ).…”

“…The most recent gene fusion databases include ChiTaRS 2.1 ( 183 , 184 ), FusionCancer ( 168 ), the TCGA Fusion Portal ( 10 ) and FARE-CAFE ( 88 ). The ChiTaRS 2.1 database of fusion transcripts and RNA-seq data ( 184 ) is the largest fusion databases and one of the few containing non-human fusion data.…”

“…These results have illuminated the roles of many gene fusions (see Section II ) and have been integrated into other resources, such as the Mitelman database. Finally, the most recently released fusion database is FARE-CAFE ( 88 ), a resource of functional and regulatory elements in fusions. This highly integrated database aims to summarize how fusions affect a variety of molecular components and activities, including Pfam domains, domain–domain interactions, protein–protein interactions and transcription factor functions.…”

Identification of a Recurrent LMO7–BRAF Fusion in Papillary Thyroid Carcinoma

“…Publicly available fusion gene databases were searched, including The Cancer Genome Atlas (TCGA) fusion gene database (www.tumorfusions.org/) (5), ChiTaRS 3.1 (http:// chitars.md.biu.ac.il/index.html) (17), and FARE-CAFÉ (18).…”

FusionHub: A unified web platform for annotation and visualization of gene fusion events in human cancer

“…Several databases have been developed that focus on information about fusion genes, their functional role, clinical association and inferred chromosomal breakpoints. Some of these databases are ChimerDB 3.0 (5 Jan 2018) (includes ChimerKB, ChimerSEQ and ChimerPUB) [ 3 ], TicDB Release 3.3 (2 Jan 2017) [ 4 ], COSMIC v83 (4 Jan 2018) [ 5 ], ChiTaRs Version 2.1 (2 Jan 2017) [ 6 ], FARE-CAFÉ (2 Jan 2017) [ 7 ], FusionCancer (3 Mar 2017) [ 8 ], Tumor Fusion Portal (4 Jan 2018) [ 9 ] and ConjoinG (3 Mar 2017) [ 10 ]. In addition to above databases, some other independent datasets are available in literature which provide list of validated fusion genes ( Fig 1 and Table 1 ).…”