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Published on: February 21, 2014
Construction of an oxidative stress-associated genes signature in breast cancer by machine learning algorithms
Daojun Hu1, Bing Qin1, Li Zhang1
1Department of Laboratory Medicine, Chongming Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Shanghai, China.
Objective:
To construct a prognostic model of a breast cancer-related oxidative stress-related gene (OSRG) signature using machine learning algorithms.
Methods:
The OSRGs of breast cancer were constructed by least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analysis. The Cancer Genome Atlas (TCGA) was used to analyse the gene expression and prognostic value. The Human Protein Atlas was used to analyse the protein expression of hub genes. Receiver operating characteristic analysis, calibration curve and decision curve analysis were used to predict the stability of this model.
Results:
The area under the curve of 1-, 3- and 5-year overall survival were 0.751, 0.707 and 0.645 in the TCGA training dataset; and 0.692, 0.678 and 0.602 in the TCGA testing dataset, respectively. Calibration plot showed good agreement between predicted probabilities and observed outcomes. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Set Enrichment Analysis (GSEA) pathway analysis indicated that multiple cancer-related pathways were highly enriched in the high-risk group. Immune infiltration analysis showed immune cells and their functions may play a key role in the development and mechanism of breast cancer.
Conclusions:
This new OSRG signature was associated with the immune infiltration and it might be useful in predicting the prognosis in patients with breast cancer.
