Pharma Focus Asia

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

Praveen Kumar Korla, Jack Cheng, Chien-Hung Huang, Jeffrey J. P. Tsai, Yu-Hsuan Liu, Nilubon Kurubanjerdjit, Wen-Tsong Hsieh, Huey-Yi Chen and Ka-Lok Ng

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.

Citation: Korla,P.K., Cheng,J., Huang,C.-H., et al. FARE-CAFE: a database of functional and regulatory elements of cancer-associated fusion events. Database (2015) Vol. 2015: article ID bav086; doi:10.1093/database/bav086

Received: April 29, 2015; Revision Received: August 14, 2015; Accepted: August 18, 2015

Copyright:© The Author(s) 2015. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Funding

Ministry of Science and Technology (MOST) of the Republic of China, Taiwan; Grant of MOST 102-2632-E-468-001-MY3 (to K.- L.N. and J.J.P.T.); Asia University (103-asia-06) and China Medical University (CMU103-ASIA-21) to K.-L.N.; Grant of MOST 102-2632-B-039-001-MY3 (to J.C.); Grant of MOST 104-2221-E-150-039 (to C.-H.H.); National Formosa University (EN103B-1005) to C.-H.H.; China Medical University (CMU103-ASIA-21) to W.-T.H. and H.-Y.C. Funding for open access charge: CMU103-ASIA-21.

Conflict of interest

None declared

Acknowledgements

We thank Professor Jim Sheu for his support on providing the use of the Metacore database. Ted Knoy is appreciated for his editorial assistance.

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