DEEPrior: a deep learning tool for the prioritization of gene fusions.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 05 2020
01 05 2020
Historique:
received:
25
10
2019
revised:
20
01
2020
accepted:
28
01
2020
pubmed:
6
2
2020
medline:
30
10
2020
entrez:
5
2
2020
Statut:
ppublish
Résumé
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. 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 data are available at Bioinformatics online.
Identifiants
pubmed: 32016382
pii: 5722203
doi: 10.1093/bioinformatics/btaa069
pmc: PMC7214024
doi:
Substances chimiques
Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
3248-3250Informations de copyright
© The Author(s) 2020. Published by Oxford University Press.
Références
Cell Rep. 2018 Apr 3;23(1):227-238.e3
pubmed: 29617662
Genes Chromosomes Cancer. 2012 Dec;51(12):1144-53
pubmed: 22927308
Bioinformatics. 2011 Oct 15;27(20):2903-4
pubmed: 21840877
Nucleic Acids Res. 2011 Jan;39(Database issue):D945-50
pubmed: 20952405
Genome Biol. 2011;12(1):R6
pubmed: 21247443
Bioinformatics. 2013 Oct 15;29(20):2539-46
pubmed: 23956304
Nucleic Acids Res. 2016 Apr 7;44(6):2859-72
pubmed: 26837576
Nucleic Acids Res. 2017 Jan 4;45(D1):D784-D789
pubmed: 27899563
Int J Mol Sci. 2019 Apr 02;20(7):
pubmed: 30987060
Nat Rev Cancer. 2015 Jun;15(6):371-81
pubmed: 25998716
BMC Syst Biol. 2014 Sep 04;8:97
pubmed: 25183062
PLoS Comput Biol. 2011 May;7(5):e1001138
pubmed: 21625565