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DEEPrior: a deep learning tool for the prioritization of gene fusions.

ABSTRACT: SUMMARY:In the last decade, increasing attention has been paid to the study of gene fusions. However, the problem of determining whether a gene fusion is a cancer driver or just a passenger mutation is still an open issue. Here we present DEEPrior, an inherently flexible deep learning tool with two modes (Inference and Retraining). Inference mode predicts the probability of a gene fusion being involved in an oncogenic process, by directly exploiting the amino acid sequence of the fused protein. Retraining mode allows to obtain a custom prediction model including new data provided by the user. AVAILABILITY AND IMPLEMENTATION:Both DEEPrior and the protein fusions dataset are freely available from GitHub at (https://github.com/bioinformatics-polito/DEEPrior). The tool was designed to operate in Python 3.7, with minimal additional libraries. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.

SUBMITTER: Lovino M

PROVIDER: S-EPMC7214024 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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DEEPrior: a deep learning tool for the prioritization of gene fusions.

Lovino Marta M Ciaburri Maria Serena MS Urgese Gianvito G Di Cataldo Santa S Ficarra Elisa E

Bioinformatics (Oxford, England) 20200501 10

<h4>Summary</h4>In the last decade, increasing attention has been paid to the study of gene fusions. However, the problem of determining whether a gene fusion is a cancer driver or just a passenger mutation is still an open issue. Here we present DEEPrior, an inherently flexible deep learning tool with two modes (Inference and Retraining). Inference mode predicts the probability of a gene fusion being involved in an oncogenic process, by directly exploiting the amino acid sequence of the fused p ...[more]

PMID: 32016382

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