An ensemble method to predict target genes and pathways in uveal melanoma

An ensemble method to predict target genes and pathways in uveal melanoma AbstractObjectiveThis work proposes to predict target genes and pathways for uveal melanoma (UM) based on an ensemble method and pathway analyses. Methods: The ensemble method integrated a correlation method (Pearson correlation coefficient, PCC), a causal inference method (IDA) and a regression method (Lasso) utilizing the Borda count election method. Subsequently, to validate the performance of PIL method, comparisons between confirmed database and predicted miRNA targets were performed. Ultimately, pathway enrichment analysis was conducted on target genes in top 1000 miRNA-mRNA interactions to identify target pathways for UM patients. Results: Thirty eight of the predicted interactions were matched with the confirmed interactions, indicating that the ensemble method was a suitable and feasible approach to predict miRNA targets. We obtained 50 seed miRNA-mRNA interactions of UM patients and extracted target genes from these interactions, such as ASPG, BSDC1 and C4BP. The 601 target genes in top 1,000 miRNA-mRNA interactions were enriched in 12 target pathways, of which Phototransduction was the most significant one. Conclusion: The target genes and pathways might provide a new way to reveal the molecular mechanism of UM and give hand for target treatments and preventions of this malignant tumor. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Open Life Sciences de Gruyter

An ensemble method to predict target genes and pathways in uveal melanoma

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Publisher
De Gruyter Open
Copyright
© 2018 Chao Wei et al.
ISSN
2391-5412
eISSN
2391-5412
D.O.I.
10.1515/biol-2018-0013
Publisher site
See Article on Publisher Site

Abstract

AbstractObjectiveThis work proposes to predict target genes and pathways for uveal melanoma (UM) based on an ensemble method and pathway analyses. Methods: The ensemble method integrated a correlation method (Pearson correlation coefficient, PCC), a causal inference method (IDA) and a regression method (Lasso) utilizing the Borda count election method. Subsequently, to validate the performance of PIL method, comparisons between confirmed database and predicted miRNA targets were performed. Ultimately, pathway enrichment analysis was conducted on target genes in top 1000 miRNA-mRNA interactions to identify target pathways for UM patients. Results: Thirty eight of the predicted interactions were matched with the confirmed interactions, indicating that the ensemble method was a suitable and feasible approach to predict miRNA targets. We obtained 50 seed miRNA-mRNA interactions of UM patients and extracted target genes from these interactions, such as ASPG, BSDC1 and C4BP. The 601 target genes in top 1,000 miRNA-mRNA interactions were enriched in 12 target pathways, of which Phototransduction was the most significant one. Conclusion: The target genes and pathways might provide a new way to reveal the molecular mechanism of UM and give hand for target treatments and preventions of this malignant tumor.

Journal

Open Life Sciencesde Gruyter

Published: Apr 10, 2018

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