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Identification of a robust subpathway-based signature for acute myeloid leukemia prognosis using an miRNA integrated strategy

Acute myeloid leukemia (AML) is a heterogeneous disease, and survival signatures are urgently needed to better monitor treatment. MiRNAs displayed vital regulatory roles on target genes, which was necessary involved in the complex disease. We therefore examined the expression levels of miRNAs and ge...

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Detalles Bibliográficos
Autores principales: Chang, Huijuan, Gao, Qiuying, Ding, Wei, Qing, Xueqin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5865743/
https://www.ncbi.nlm.nih.gov/pubmed/29570744
http://dx.doi.org/10.1371/journal.pone.0194245
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author Chang, Huijuan
Gao, Qiuying
Ding, Wei
Qing, Xueqin
author_facet Chang, Huijuan
Gao, Qiuying
Ding, Wei
Qing, Xueqin
author_sort Chang, Huijuan
collection PubMed
description Acute myeloid leukemia (AML) is a heterogeneous disease, and survival signatures are urgently needed to better monitor treatment. MiRNAs displayed vital regulatory roles on target genes, which was necessary involved in the complex disease. We therefore examined the expression levels of miRNAs and genes to identify robust signatures for survival benefit analyses. First, we reconstructed subpathway graphs by embedding miRNA components that were derived from low-throughput miRNA-gene interactions. Then, we randomly divided the data sets from The Cancer Genome Atlas (TCGA) into training and testing sets, and further formed 100 subsets based on the training set. Using each subset, we identified survival-related miRNAs and genes, and identified survival subpathways based on the reconstructed subpathway graphs. After statistical analyses of these survival subpathways, the most robust subpathways with the top three ranks were identified, and risk scores were calculated based on these robust subpathways for AML patient prognoses. Among these robust subpathways, three representative subpathways, path: 05200_10 from Pathways in cancer, path: 04110_20 from Cell cycle, and path: 04510_8 from Focal adhesion, were significantly associated with patient survival in the TCGA training and testing sets based on subpathway risk scores. In conclusion, we performed integrated analyses of miRNAs and genes to identify robust prognostic subpathways, and calculated subpathway risk scores to characterize AML patient survival.
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spelling pubmed-58657432018-03-28 Identification of a robust subpathway-based signature for acute myeloid leukemia prognosis using an miRNA integrated strategy Chang, Huijuan Gao, Qiuying Ding, Wei Qing, Xueqin PLoS One Research Article Acute myeloid leukemia (AML) is a heterogeneous disease, and survival signatures are urgently needed to better monitor treatment. MiRNAs displayed vital regulatory roles on target genes, which was necessary involved in the complex disease. We therefore examined the expression levels of miRNAs and genes to identify robust signatures for survival benefit analyses. First, we reconstructed subpathway graphs by embedding miRNA components that were derived from low-throughput miRNA-gene interactions. Then, we randomly divided the data sets from The Cancer Genome Atlas (TCGA) into training and testing sets, and further formed 100 subsets based on the training set. Using each subset, we identified survival-related miRNAs and genes, and identified survival subpathways based on the reconstructed subpathway graphs. After statistical analyses of these survival subpathways, the most robust subpathways with the top three ranks were identified, and risk scores were calculated based on these robust subpathways for AML patient prognoses. Among these robust subpathways, three representative subpathways, path: 05200_10 from Pathways in cancer, path: 04110_20 from Cell cycle, and path: 04510_8 from Focal adhesion, were significantly associated with patient survival in the TCGA training and testing sets based on subpathway risk scores. In conclusion, we performed integrated analyses of miRNAs and genes to identify robust prognostic subpathways, and calculated subpathway risk scores to characterize AML patient survival. Public Library of Science 2018-03-23 /pmc/articles/PMC5865743/ /pubmed/29570744 http://dx.doi.org/10.1371/journal.pone.0194245 Text en © 2018 Chang et al http://creativecommons.org/licenses/by/4.0/ 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 use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Chang, Huijuan
Gao, Qiuying
Ding, Wei
Qing, Xueqin
Identification of a robust subpathway-based signature for acute myeloid leukemia prognosis using an miRNA integrated strategy
title Identification of a robust subpathway-based signature for acute myeloid leukemia prognosis using an miRNA integrated strategy
title_full Identification of a robust subpathway-based signature for acute myeloid leukemia prognosis using an miRNA integrated strategy
title_fullStr Identification of a robust subpathway-based signature for acute myeloid leukemia prognosis using an miRNA integrated strategy
title_full_unstemmed Identification of a robust subpathway-based signature for acute myeloid leukemia prognosis using an miRNA integrated strategy
title_short Identification of a robust subpathway-based signature for acute myeloid leukemia prognosis using an miRNA integrated strategy
title_sort identification of a robust subpathway-based signature for acute myeloid leukemia prognosis using an mirna integrated strategy
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5865743/
https://www.ncbi.nlm.nih.gov/pubmed/29570744
http://dx.doi.org/10.1371/journal.pone.0194245
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